But dude, we already know he's signed as a regular for S.4 (assuming it goes, of course). He had just signed, THAT DAY, back in November when he came to the Burbank con. And he said at that time that they had found a story for him that was separate to him being Kara's love interest.

So, see that just adds to my theory. He was expected to be in only the first few of the season, to finish off the Kara/Anders-in-the-occupation thing at the beginning (through Collaborators,is my guess). And then, somewhere along the line, the PTB were designing the season finale and this thing they're planning to do with Kara, and I suspect they decided that it was going to play better with Sam, rather than Leoben. So Sam's role has been clicking along as part of the Quadrangle, and Leoben has practically dropped out of sight, all so we can get to Sam's new deal at the end of the season. If it's NOT him being one of the Five, I've got no clue, but it SEEMS (perhaps) to be connected to this wacky "Let's hire CKR for eight episodes and yet wind up with two lines" thing.

Or, they're purposefully cutting Leoben out so that his "return" is that much more dramatic, which is kinda goofy, but possible. Dunno.