I’ve seen issues with the M03/M05 on this forum. The usual solution is to use inline commands instead. That is, use the ‘S’ parameter of the G0 and G1 g-codes to specify the laser power. Try running the test file that Ryan created in the first post of this topic.
Note that like you, the others having problem with the M3/M5 were having quality issues. I’m not sure why since they should work, but the M3/M5 commands are a bit complex since, depending on the firmware settings, the expected values change. I’m betting there is a bug at the root of the problem.
As for the fan pins, I’m guessing that you did not supply he right parameter for the specific fan pin pair you used, but that is only a guess. I’m sure we could get it working, but from everything I’ve read on this forum, inline commands are the way to go.