My steam isn't in sync with my Skyrim, for example on one of my characters i have over 100 hours of game play, but my steam says 50.
also all of the quest line achievements are locked even though i have finished all of them.

How long you've been using steam ? I used steam 2 days and I noticed how MANY things are ****** up in steam. Steam is a broken program which I hate so much.
I suggest you should try to contact support if it's bothering too much, but do not hope to get any good answers from them.

thanks for that but i suppose i'll just have to forgo bragging rights over achievements. if it didn't screw up i would have all of them.

Are you sure, you're not playing in offline mode? You have to be online for your stats and achievements to be updated. Also make sure your window's/internet security's firewall is not blocking steam.exe.

Achiemevents not registering seems to be a common bug: I managed to get Head of Thieves, but not joining the guild! Went right through the CW quest line and didn't get those ones either. I broke out of jail, and even got the bounty for doing it, but never got that achievement. There's a lot of comments about it on t'web. The option seems to be carry out that achievement again.