This has probably been asked before but in case it is just me, why don't all my subscriptions appear when i hit the MY SUBREDDITS drop down thing? oh and the missing ones are not on the top side list either.

You can only see 50 at once (or 100 with gold). The front page shows a randomized selection of 50 of your x subscriptions. The list you see is the subreddits that are currently active. The only way you'll always see them all is if you have 50 or less.

I was just figuring this out myself. Click MY SUBREDDITS, then EDIT SUBCRIPTIONS in the drop down list. Finally go to the my subreddits tab. EDIT: Also, you can just press EDIT instead of the second sentence.

Since Friday, I can view my subscriptions under "Hot" but if I click "Top" posts for "Today" it says no new posts.