So I'm bumping this thread up because I'm experiencing the same issue with multitrack tracks being out of sync with all .wav files at 48,000 Hz. Downsampling them to 44,100 seemed to work, but this feels more like a bandage for us. We've been working with 48,000 near exclusively and now have to add "downsample bounces to 44,1" to our workflow — every time we have to make changes (which tends to be more frequent when we're starting out with new material) we have to downsample as well.