Have you tried playing back the tracks out of another source or system ??
Like a different sound card or interface . If not try burning a stereo mix down and playing them in CD player .
I have a simular problem with a Tascam US -122 usb interface .
I get skips or dropouts in random spots on playback but it still records with no problem I just have to use a line out from my soundcard to hear my backing tracks and for mixing .
Someday soon I hope to step up to a Presonus 8 i/o firewire interface .
I get this same problem, only with me it happens with vocals. I dont know if its casue I have the mic up too loud, or if Im recording too many vocal tracks. Like run thrus and and such