Yes I have the quests active. Right now the ones I have no marker for are:

Miscellaneous: Clear Redbelly Mine of Spiders
The Golden Claw: Locate owner of Golden Claw
Message to Whiterun: Assist Balruug with Dragon Threat

Now possibly the last one I shouldn't have a marker for, but the first one I definitely should. How on earth do I find Redbelly Mine otherwise? I've found just about every marker in the rift but can't find that mine. >.> Yes I have both Misc. selected AND the specific quest. No marker... on map or compass.

Really annoying bug - they are starting to add up for us PC users. >.<

Well. Still happening.

Today I was doing an Amulet quest where you gather 3 pieces and reforge. One of the locations was not showing up on my map. It was an island in a lake it said in the book. Well I searched all over, and finally found it. And when I did, all of a sudden the quest marker showed up.

So this is a definite BUG.