Wow, those are powerful motors.
I think this chart shows the potential of how your boards can get fried not only on inrush current, but during operation as well.
You mentioned earlier that 40A registered on inrush current with no load, that's 13.3333 x the no load normal operation of about 3A.
You see with just 25in/lb torque (load) that doubles to 6A. The threshold is around 103 in/lb torque (load) @ 12A because changing directions would double that up with 206 in/lb torque (load) nearly 20A. Which is just under the recommended 23A safe zone for the boards with no heat sinks or cooling fans.
IF the 200A is the threshold for inrush current limitation for a fraction of a second during start of motor,
we are
guessing that 13 is the ratio of inrush current spike based on your zero load readings.
6A (25in/lb torque)x 13 = 78A <---- Much safer
12A (103in/lb torque) x 13 = 156A <--- dangerously high
20A (202in/lb torque) x 13 = 266A <--- fry board
So the last riddle to solve is how much torque is added to the motors when attached to your simulator to effectively spike your inrush current high enough to fry your boards. This theory shows just over 105in/lb torque could potentially do it.
It's a safe bet that you are probably 50in/lb - 75in/lb (torque) under normal operation, since you mentioned using a 15A fuse when you were able to operate the system. Changing directions would put you in the 100in/lb-150in/lb (torque) range which is brushing up against the 15A fuse limit. Which is also showing you could theoretically be crossing the threshold for 200A+ on inrush current.
In ANY case, these motors will not stall before your boards fry. They are VERY powerful, and can pull nearly 100A with up to 1,000 in/lb torque.
You MUST have some sort of limiter in your circuit if you choose to continue using these motors and those boards.
One last note... The fuse you are using may not be sufficient as a safety device either... If the fuse blew and the board still fried, that could be an indication that the current is arcing through the fuse and frying the board as well... Since I don't know the schematic to how you have your battery and boards wired, I can't really comment on this topic too much. But certainly another issue that needs some attention as well.
This site is for amplifiers and stereos but still good information about fuses there...
http://www.bcae1.com/fuses.htm