Not the best workaround -> Don't minimize the swtor window -> Bring the swtor window to the foreground If you cannot "afford" to bring the swtor window to foreground (your other apps need to be active), then you have to run swtor and the bot in a virtual machine software.
Tried that, didn't help. Still got the bot standing at the vendor trying to repair. But only sometimes.... sometimes it just continues on without any problems. Also; most virtual machines have very crappy 3D graphics support, thereby becoming a non-option.