What USB thumb drive and configuration are you specifically using? I use a 32 GB Toshiba TransMemory Rev 1.00 formatted as FAT32 with 32k clusters, and the opening FMVs of my games run perfectly. Fire Emblem: PoR, Zelda Collector's Edition, WarioWare, and Twin Snakes, (on deflated isos, no less) give me no trouble whatsoever on Nintendont. And neither do Crystal Chronicles, Double Dash, Melee, Colosseum, XD, or any of my other games on Devo. In short, FMVs run perfectly on my <£10 flash disc. On both actual Wii and vWii.
Maybe you just have a chip with bad read speeds, or you're severly fragmented? Fixing fragmentation on flash-based discs is best done by moving all the data off the disc, wiping it (single-pass), and then putting it all back. Don't use a defragmenting program, as they're designed for hard discs, as they don't use wear-leveling. Obviously, this wears the drive a little.