Actually it should. Hard to help without being able to reproduce it.
You should check your CGI logs to see what errors might be being generated. Perhaps that may shed some light on the problem. Also give teh 1.2 release a try and see if it makes a difference.
ok... i figured this one out... I had the original files (avi's and mov's) with the flv's. Once I took those away, the problem was solved.