Did you look in the Subscriber Trace to see the events coming in and how they're evaluated?
Based on the rule, it looks like it works as designed. You set the comment, which generates an entry changed event. Workflow starts, reads the comment and modifies the document to set the Comment History field. This action generates the second Entry Change event. At this time, the comments field is not empty yet, because there's a decent chance Workflow reads the field values again before the Clear Fields activity runs.
You should change the connection profile in the workflow to something other than Admin and then exclude actions of that user in the starting rule. Having a dedicated user for Workflow would help troubleshooting situations like this by making it clear which are your actions and which ones come from Workflow.