It is still not clear if you have separate projects sharing common libraries or if you have separate libraries as well, a feature introduced in verion 3.
I suspect you have common libraries, and somehow your data got corrupted so that place fields are pointing to the wrong places in the common library. There are a couple of utilities that can try to repair or reindex your database, and that may solve your problem.
If your data really has changed, you may have a lot of work cut out for you to correct all the places. I don't know if that would be easier to do in UFT or in TMG. You could post your problem on their board, asking how difficult it would be in the two products. There are lots of UFT experts who are now TMG users, so you have a good chance at getting an answer.