In deed your second load out was probably affected by this bug. I discovered it my self on Friday while doing testing for CR 2.0. If you unload and then reload the hacker ability your hacker style will be as if it wasn't leveled. The work around is if you have to unload the Hacker ability then just use the Execute Program ability instead. By reload both Execute Program and Hacker your Hacker style will be normal.
The Hacker ability and Execute Program are trying to provide the Hacker style so the system is getting confused.
