He does know what happened between Kota and Starkiller during TFU1 and not that much has happened between them in TFU2. Plus come on, Starkiller's been killed, revived (twice, actually), tortured, brainwashed, cloned, and god knows what else. Of course he's going to act a little weird.
As for Kota sensing a dark sider, in my opinion Starkiller is and always has been one. Plus Kota's an old fool that can't even tell the guy he's sitting next to isn't a Jedi.