Hello Thomas,
First congratulation for this awesome project you are kind enough to share with us.
I made an astroEQ based on the mega2560 today , this won't be mine as i already have an azeq6 electronic in my 720:1 losmandy g11 but a friend of my local club.
To make it more conveniant i rerouted some pin when i designed the board .
So i used the source code in github to modify the pinout.
Then when i started to use it, i noticed some freezing as well as unsmooth moving on axis.
To make long story short, after some trying i replaced the original Pinmappings.h and the problem persisted (i can tell it thanks to the status light wich froozen).
Finally i uploaded the hex file that is in the config tool and the status led is no more freezing .
The stock source code firmwire isn't working as expected, but the hex firmwire is working fine.
Should i deduce that the source code published isn't the lastest revision?
All the best
Nicolas