From the Announce forum:

"there's a fixed empegClone file available at the usual spot. There were some problems with the one included previously that could cause some fairly heinous problems."

I think you experienced those fairly heinous problems. Any "lost" tracks should be in Unattached Items, but obviously reorganising them could be a pain.

Sorry for the hassle. Obviously we didn't experience this problem in our original testing, but we did fix the problem as soon as it was reported.

Rob