Sorry, I mean that they're COMPLETELY different. As in, Arduino is uploading a version of the program that is several revisions previous to the source that I'm editing. The old and new versions have serial output so I can verify that the program is running, but its output is not possible based on the source code that's currently being shown by the IDE. After modifying and saving my sketch, and finally re-installing Arduino004, the source and compiled code started agreeing again. I'm starting to wonder if it has something to do with code size, since as I near the 7K limit, it behaves more strangely.