Timing Errors

I've been using Sonic Foundry Vegas, and Sonic Foundry Acid for a while now. They worked beautifully for a while, then out of nowhere heres what they do now: I record over something, hit it perfect; then i play it back and listen...everything is like displaced by like 12 miliseconds or something. I have no clue what happened. No matter what i do now, it displaces everything. In order to record, i've had to use what i normally use for editing (Sound Forge) and put my guitar sound into 1 preamp channel, and a backing track into my other preamp channel, and make a stereo recording with my guitar coming out of left, and backing coming out of right. Anyone else use these programs and expierience the same? Does it have something to do with that "Time/sync" or "time code" options? Im rather frustrated.