Only thing I can think of is that perhaps the animation you're using for the gel is interlaced and your Carrara project is not.  (Carrara can render interlaced video, but it's not the default.)  So, maybe Carrara is getting hung up on a field as opposed to frames? 

Just grabbing at straws, there.  I haven't had this trouble, though I've used movies for gels before.  (In C4, not C5, but I can't imagine they'd go backwards in usability....)

Dex