Since it's the other major common part between the test setups, it sounds like the motor has a problem. Could be a winding fault, or a sensor fault, or wiring issue, such as interference between phases and sensor signals, connection faults, etc.
Without knowing the complete details of the system and all the parts used so far, and the specifics of the test situations where the problem occurs, it's difficult to get specific with solutions.
I'd also recommend editing your title to reflect the actual problem--what it sounds like now with "3 x throttle problem" is that you have a problem running three throttles at once, or a problem with three different throttles, etc. More people with useful info for your situation might look at the thread to help if it were better-titled.
Oh, also, a battery issue could cause problems of all sorts, depending on the controller design and response to the issue--for instance, voltage sag from a battery problem can cause a controller's soft-LVC to turn down the power or run the motor differently to prevent current draw that causes that sag. This is something you'd have to diagnose by testing individual battery parts while loading it at least as heavily as it was during the problem; if that only happens while riding, you may have to make a DIY load you can use on the test bench.