I pretty much fixed the issue by wiping the ipod, and then re loading all the files, but only after closing and restarting itunes.
that seemed to fix the time issue, and most of the gaplessness. I'm using a touch now, and havent experienced any issues.
Also, ALWAYS disconnect the ipod using the icon in itunes or it messed up the DB every time for me.. and i got all kinds of weirdness
Oh. I see you're using ALAC.. I converted to 256 AAC and can't really tell a difference most of the time.. unless i listen real hard to music i know inside out.. I can tell, but it wasnt worth the effort for me.
oh and i converted my flacs to WMA lossless to keep it gapless and lossless, then dropped those into itunes to get 256 AAC, and then when i'd added album art and tidied any stray tags up, closed itunes.
reopened it, then manually added the files to the ipod and it worked perfectly
long process, huge pain in the wahoo, but now it works.
Seemed to me that DB poweramps FLAC > ALAC coding is a bit funky.. and I tunes seemed only to get track lengths right( and threfore gapless) when it encoded it itself. (which takes forever - single threading on a quad core.. ugh)
and as itunes can't read flac(!), it needed to be lossless, with tags, so WMA lossless it was. Still couldn't get it to convert to ALAC though so i went higher bitrate AAC. It's pretty good
So now I got gapless but not lossless. I'd rather have the gapless though.
sorry for rambling