This works, however I'm curious as to why when the Checkbox variable is used to save metadata field data to a multi-value field it shows up as a single value with a string of comma(space) separated values... which then needs to have the additional spaces removed in order to use the values back to checkbox field.

Will,

I'm running into a very similar thing.  From a workflow I'm retrieving the value(s) of a checkbox on a form.  Then I'm loading those values to a separate form to prepopulate the same checkbox on a new form.  Only the first value that was checked, of nine possible, is actually loading.  I'm pretty sure I have it narrowed down to the spaces between values.  

Were the values you load to the checkbox from an existing checkbox?  Or did you just create your own list?

Jamie,

It's been a while, but I believe the process was that one forms process saved to the repository with a checkbox field being saved to a metadata field, then a workflow process would run which checked for forms saved to the repository, pulled the metadata value from each form and used that to populate a checkbox within a collection in the new form started by the workflow... 

So Form Process A to Repository Metadata to Workflow variable to Form Process B.  So simple answer is that yes it was from an existing checkbox, though it was stored in a few places in between steps.

Hope this helps.