Sorry about the links, fixed.
I'm powering the motor from 2 16340 batteries (3.7V each). I've tried powering both arduino and H-bridge from the batteries and just the H-bridge with the grounds connected. Makes no difference.
The motor has no caps, it looks like this. I'll try soldering some caps but I'll have to go shopping first.
AFAIK there are no jumpers to set the power source.. Shouldn't be a problem since the only wires connecting the arduino to the bridge are the 3 signals and the common ground. That 5V_EN jumper is to disable the regulator (haven't tried that since I'll need to supply 5V externally).
I might try to add that missing cap, might help since it's between the 5V and gnd rails.
I also noted that this board has pull-up resistors for every signal rail, most can be disabled but the ones for the enable pins cannot. Can this get interference back to the Arduino? Should I cut the rails?