Here's my theory, based on this video:
When Daniel went to spend a little quality time at the OpA Day Spa & Brainwashing Center, his caretakers took care to implant some conditioning that would make him useful to them later. They had to do this deeply enough so that Daniel wouldn't know himself that it had happened, because a) Bree would probably notice if he started acting like Gemma, b) Tachyon could get ahold of him, c) Daniel's not very good at hiding things. This explains why Daniel can't really remember what happened to him during his stay.
Conclusion: Daniel is a sleeper agent (attn followers of Battlestar Galactica--think Boomer) who doesn't even know he's been recruited by the Order.
Jonas, on the other hand, has been a member of the Order all along--I have always said that this was the case anyway.
He may or may not know that Daniel has been conditioned, although I suspect he does. He may or may not know Daniel's trigger, although I suspect he doesn't. His orders were to keep B&D in one place at all costs, until Tachyon showed up. Then, he was told to pick up and move quickly to somewhere she wouldn't be able to find so easily (maybe this order came when the Watcher showed up at the house and declined to hit Jonas in the face, as he richly deserves?). Hey presto! Jonas suggests they go up to his family's magical secluded cabin in the woods, where he blatantly violates the no-cell-phone rule (to communicate with whom, I wonder?).
Now, Jonas is sewing dissenion between B&D, letting Bree go off the handle and take it out on him even as he softens Daniel up--maybe to make the conditioning come out more fully.
Theory #2:
On the subject of the distorted audio, there are two things going on here. One is the plot, which involves the characters Daniel and Jonas having a "discussion." In this discussion, they say some things influenced by the Order, possibly without knowing it. The other thing going on is a meta tool to give us a clue to what's going on. This is done by putting strange audio over the parts we should be listening most closely to. The characters don't know that the strange audio is there, even though they're supposed to have edited and uploaded the vid. There are two explanations for this, one in game and one meta.
In-game: Daniel is programmed to do this and so he doesn't realize that he's doing it.
Meta: We just need to accept that sometimes the PM does things for us to notice that the characters don't see.
"A step in the right direction? It only turns out to be so if you're willing to step much further."
-Samuel R. Delany
