Hi Haris,
This still doesn't answer my question. The question really is how does the FILENAME part look like exactly. Doesn't matter if you used \include or \input, but the script used to be a bit picky about the FILENAME. For instance it used to be that it would only work with files with extension .tex, though that was recently fixed.
Needless to say, Haris, this answered my issue. The template I was using had quotes around the filenames, on removal, it all works fine. I'm not sure whether the quotes are correct style or not, but this was the problem, everything works now.
Perhaps if quotes are common, then these can be set to be ignored by TextMate?
Thanks again for your efforts!
Suhaib.