Hi Andres,
welcome to TextMate!
It is surprising that the \ref commands don't work, for the cite command we've had some problems related to malformed bib files. Can you send me a small test file demonstrating the problem, accompanied by a test bib file, and I can see what is going on?
Does label completion work for you on single files? I.e if you have a file, SAVED, with contents:
\documentclass{article} \label{hi} \ref{}
And you press opt-esc with the caret inside the {} in the ref, what happens? If this works, then please send me some test files that have problems.
Haris Skiadas Department of Mathematics and Computer Science Hanover College