Phil,
Thanks, I did discover that work around. It is just strange that I had not had this problem at all in the past. I have exported hundreds of .wmvs directly from FCP and Compressor with no issues. Today it seems as if it just decided to stop working. Hopefully when I get to the office tomorrow, it will have resolved itself.
I did try un-installing and re-installing flip4mac, trashing the FCP prefs, and rebooting.
Thanks!