I've been having similar problems trying to sync my Timefactor up to a drum machine to get loops going in time, using the tapecho model. I thought that I should add that the problem doesn't seem to me to be in the midi sync receiving, rather the way the delay time and the midi sync work together.
After I noticed it wasn't syncing up I disconnected the midi lead and tapped the tempo in manually. I got the same value tapping in as I'd gotten with the midi sync signal, and the tap and tempo lights were flashing in time to the drum beat I had going.
I tried some basic stuff like setting a 1 bar delay time and just clapping into the mic I had set up into it on the 1, when the tempo light on the TF flashed. Not only were the delays not in time with the drums but they weren't even in time with the flashing light on the TF. This is what led me to think the problem isn't with the receiving of sync after all, but rather the calculations the TF is doing to work out delay time from the tempo. It almost seems like it's synced to 15/16 instead of 16/16.
Anyway, hope that helps you guys sort this out. My OS is 2.0.3.