Oh so THAT's where it's from
 

It's only half an hour ago, watching the first ever Star Trek movie for the first time in years that I realised the TNG theme music is the music from the movie.

Anyone else have any experience of suddenly realising where you heard a tune before or noticing connections between sequels years after the event or is it just me being unobservant?

Well, there's a bit in the opening music for Xenosaga I that quotes stuff from the opening for Xenogears that I didn't notice until I had an mp3 player (which was after the third Xenosaga came out, and I devoured both Xenosaga I & 'gears' OSTs)