In Shadowmire after I get the cypher rune...a gate is supposed to open when I backtrack a little ways...I'm pretty sure I know what gate this is and for some reason it isn't opening...Any suggestions?! I already have the rune and have completed all tasks.

That's the first stage Rynn goes into without Arokh, right?
It's been a long time since I've played, but you might have to backtrack all the way to the beginning of the swamp to get back out, because I think you're supposed to talk to the dude who lost his daughter again now that they've been reunited.
Not sure if you get a reward from him, though you probably do.
Oh, and I seem to remember some sort of chamber there you can get the earth sword from, where you get locked in and have to fight a bunch of skeletons before you can leave with the sword.