Temporarily commenting all the code makes the submissions more consistent. May be my JavaScript have some problem?
I perform lookup to set values to hidden fields, then use those fields to set values for checkboxes.

console.log("DEBUG")

const soNumber_fieldId = 2;
const for_fieldId = 3;

const req_OutlinePackageA_fieldId = 14;

const req_TestReports_fieldId = 18;

const req_InstructBooks_fieldId = 19;

const req_SparePLU_fieldId = 20;

const req_SolidWorks_fieldId = 22;

const req_Other_fieldId = 23;

const req_Special_Instruction = 60;

var requirements = {
    value: [],
    otherChoiceValue: ""
}

var isBinding = false;

var requirementsReady = false
const getRequirements = (fieldId, reqValue) => {
    var req = LFForm.getFieldValues({ fieldId: fieldId });
    if (!req) return;

    if (req.toLowerCase() === 'true') {
        if (!requirements.value.includes(reqValue)) {
            requirements.value.push(reqValue);
        }
    } else if (req.toLowerCase() === 'false') {
        requirements.value = requirements.value.filter(x => x !== reqValue);
    }

    else if (req.trim() !== '') {
        if (!requirements.value.includes("_other")) {
            requirements.value.push("_other")
            requirements.otherChoiceValue = req;
        }
    }
    else if (req.trim() === '') {
        requirements.value = requirements.value.filter(x => x != "_other")
        requirements.otherChoiceValue = "";
    }

    LFForm.setFieldValues({ fieldId: 4 }, requirements)
    requirement_snapshot = requirements
}

LFForm.onLookupTrigger(function () {
    LFForm.setFieldValues({ fieldId: 39 }, "")
    requirements.value = [];
    requirements.otherChoiceValue = "";

    requirementsReady = false;
}, { lookupRuleId: 1 })

LFForm.onLookupDone(function () {


    var soNumber = LFForm.getFieldValues({ fieldId: 2 })
    var taskType = LFForm.getFieldValues({ fieldId: 3 })
    if (soNumber === '' || taskType === '') {
        return
    }
    requirementsReady = true
    checkForModifications()
}, { lookupRuleId: 1 })

function checkForModifications() {
    if (!requirementsReady) return
    const revision = LFForm.getFieldValues({ fieldId: 75 })
    const currentReqs = LFForm.getFieldValues({ fieldId: 4 })
    const reqUnchanged = arraysEqualUnordered(requirements.value.filter(x => x != '_other'), currentReqs.value.filter(x => x != '_other'))
    const otherUnchanged = requirements.value.includes('_other') || requirements.value.includes('_other')
    const otherValueUnchanged = requirements.otherChoiceValue == currentReqs.otherChoiceValue
    const specialInstructionUnchanged = LFForm.getFieldValues({ fieldId: req_Special_Instruction }) == LFForm.getFieldValues({ fieldId: 5 })

    const isDirty = !(reqUnchanged && otherUnchanged && otherValueUnchanged && specialInstructionUnchanged);
    if (revision && revision != '' && isDirty) {
        LFForm.setFieldValues({ fieldId: 39 }, "Modified")
    }
    else if (isDirty) {
        LFForm.setFieldValues({ fieldId: 39 }, "Creating")
    }
    else {
        LFForm.setFieldValues({ fieldId: 39 }, "")
    }
}

LFForm.subscribe('fieldChange', () => getRequirements(req_OutlinePackageA_fieldId, 'OutlinePackageA'), { fieldId: req_OutlinePackageA_fieldId });
LFForm.subscribe('fieldChange', () => getRequirements(req_TestReports_fieldId, 'TestReports'), { fieldId: req_TestReports_fieldId });
LFForm.subscribe('fieldChange', () => getRequirements(req_InstructBooks_fieldId, 'InstructBooks'), { fieldId: req_InstructBooks_fieldId });
LFForm.subscribe('fieldChange', () => getRequirements(req_SparePLU_fieldId, 'SparePLU'), { fieldId: req_SparePLU_fieldId });
LFForm.subscribe('fieldChange', () => getRequirements(req_SolidWorks_fieldId, 'SolidWorks'), { fieldId: req_SolidWorks_fieldId });
LFForm.subscribe('fieldChange', () => getRequirements(req_Other_fieldId, 'Other'), { fieldId: req_Other_fieldId });

LFForm.subscribe('fieldChange', () => checkForModifications(), { fieldId: 4 })
LFForm.subscribe('fieldChange', () => checkForModifications(), { fieldId: 5 })
LFForm.subscribe('fieldChange', () => checkForModifications(), { fieldId: 6 })

function arraysEqualUnordered(arr1, arr2) {
    if (arr1.length !== arr2.length) return false;
    const sorted1 = [...arr1].sort();
    const sorted2 = [...arr2].sort();
    return sorted1.every((val, index) => val === sorted2[index]);
}

LFForm.onFormSubmission(function () {
    if (!validateDesignFreezeExists()) {
        return { error: "The design has been frozen. You can no longer submit design review/freeze request(s)." };
    }
    if (!validateDMI()) {
        return { error: "You must use the SO Number/Quote with letter for DMI. Eg: 25-12345/WQ123456. Please check your input." };
    }

    if (!validatePrototype()) {
        return { error: "You must use the SO Number with letter for PROTOTYPE. Eg: 25-12345A. Please check your input." };
    }
    if (!validateDesignFreeze()) {
        return { error: "The SO Number must have AT LEAST ONE design review to be able to submit the design freeze." };
    }
});

function validatePrototype() {
    var task = LFForm.getFieldValues({ fieldId: for_fieldId })
    var soNumber = LFForm.getFieldValues({ fieldId: soNumber_fieldId })

    var soNumberWithLetterPattern = /^\d{2}-\d{5}[A-Z]$/;

    if (task.value.includes("Design") && !soNumberWithLetterPattern.test(soNumber)) {
        return false;
    }

    return true;
}

function validateDesignFreeze() {
    var task = LFForm.getFieldValues({ fieldId: for_fieldId })
    try {
        var designReviewRevisions = LFForm.getFieldValues({ fieldId: 68 })

        if (task.value === "Design Freeze" && designReviewRevisions.length <= 0) {
            return false;
        }

        return true;
    }
    catch (error) {
        if (task.value === "Design Freeze") {
            return false;
        }
        else return true;
    }
}

function validateDesignFreezeExists() {
    try {
        var task = LFForm.getFieldValues({ fieldId: for_fieldId })
        var designReviewTaskTypes = LFForm.getFieldValues({ fieldId: 67 })

        console.log(designReviewTaskTypes)

        if ((task.value === "Design Freeze" || task.value === "Design Review")
            && designReviewTaskTypes.includes("Design Freeze")) {
            return false;
        }
        return true;
    }
    catch (error) {
        return true;
    }
}

function validateDMI() {
    var task = LFForm.getFieldValues({ fieldId: for_fieldId })
    var soNumber = LFForm.getFieldValues({ fieldId: soNumber_fieldId })

    var soNumberTrimPattern = /^\d{2}-\d{5}$/;

    if (!task.value.includes("Design") && !soNumberTrimPattern.test(soNumber)) {
        return false;
    }

    return true;
}

LFForm.onFieldChange(() => {
    var task = LFForm.getFieldValues({ fieldId: for_fieldId })
    switch (task.value) {
        case "Approval":
        case "Record":
        case "Final As-Built":
            LFForm.setFieldValues({ fieldId: 78 }, { value: "DMI" })
            LFForm.setFieldValues({ fieldId: 39 }, "Creating")
            break;
        case "Design Review":
        case "Design Freeze":
            LFForm.setFieldValues({ fieldId: 78 }, { value: "Prototype" })
            if (task.value.includes("Freeze"))
                LFForm.setFieldValues({ fieldId: 39 }, "Creating")
            break;
    }
    LFForm.setFieldValues({ fieldId: 4 }, { value: [], otherChoiceValue: "" })
}, { fieldId: for_fieldId });