Unmodified files hanging out in Works in Progress

System

I'm seeing something odd in CCSTD. My Works in Progress portlet has many files in it which appear with the pencil (modified) icon. If I try to submit them, it gives me the "The file has not been changed since the last submit. There is no need to resubmit the file. " error. If I click next anyway, it takes me back to CCSTD and the file is still there. If I view the properties on the file, it shows the version as 1 (not 1+). So, anyone have any ideas why it's in WIP and what I can do to get rid of it? Any chance this is related to the renaming of folders and such that I recently did?