I've been reading in quite a few places that lots of quests are glitchy and it sounds like in a lot of cases if you discover a new location and clear it before getting any quests that are associated with that area that you won't be able to properly complete them later on. Can anyone shed any light on this? Is it best just not to go into a place unless a quest directs you there?

Probably isn't. Although if you're careful and know what what to look for you should be fine in most cases. For example, there was some nameless ruin I went into, in some chest there was a iron sword (think it was an iron sword), but it was named. Can't remember the name of it now but it was [Name]'s Sword, so it obviously belonged to someone with that name. Those are the types of things that are quest related. Anyway to make sure I saved the game, picked it up and tried to drop it. Sure enough it was a quest item and couldn't drop it. So I reloaded, guessing I would come across the quest it related to later on.

Shouldn't happen but there you have it, pretty stupid. I still end up with quest items in my inventory mind you, Staff of Charming...sounds pretty generic but, it's a quest item apparently.

Anyway just be careful what you pick up. I don't use take all anymore.