"I'm working to change your accommodations," he says a shade too quickly in an effort to not make everything he says sound suspicious and multilayered. And that's not strictly speaking a lie - Daniel is working to change Seth's accommodations, just not to a nicer cell so much as someplace far away from the base and everyone in it.

"You'll only get a transfer if you continue to be agreeable." In other words, sit tight and don't draw negative attention, but that much is fairly obvious, so it all just sounds redundant at this point. Daniel's reluctant to leave as he has no idea when they'll be able to communicate again.