It seems to work fine for me. I would try checking your line endings, make sure you are using the newest version of TextMate, make sure you have Regular Expression checked in the find box, and make sure there isn't any whitespace at the end of the lines.
I piped the output of a command to a text file as such:
sudo dscl . -list /Users UniqueID ~/Desktop/unique_id.txt
and opened the file with TextMate:
open -a TextMate.app ~/Desktop/unique_id.txt
I did a simple regex lookup " 9$" (looking for an ID of '9') and hit the Find All button (i.e. the operator ?). This yielded 0 results however when I hit the next button, it would have a result.