[filmixer]

>have you come across this where there is this extra bit at the beginning of the file?<
No. If I zoom the view in to the sample level, my files start right at 1:00:00:00. I've also never had a file I've sent to a Avid or Final Cut HD bay not spot properly or drift.

>Makes it very annoying when you pull the stems into a new session, line them up on the Grid and the 2pop is a quarter-frame off.<
I never use Grid mode, but if you spot the files using "Original Time Stamp" or Control drag them onto the timeline with the cursor at the exact code you want, they should spot perfectly. As far as your 2 pop, if it's late, was it on a dialog track that had a number of plugins and maybe routed through a couple of bussing chains to it's stem track? A little latency might have cropped up.