Hi Tom,
I have just tried configuring my original Arduino Mega Astro-EQ with version 8.05 of the configuration utility and following configuration the AstroEQ does not work correctly with EQMOD. If you try connecting to EQMOD, either via ASCOM Toolbox or at the end of the config utility, the status light starts to flash rapidly and EQMOD is unresponsive. Sometimes you get a timeout error. After EQMOD is closed the status light continues flashing rapidly. The only way to stop this is to disconnect power and USB.
Reverting to Version 7.4 of the config utility fixes the issue after you update firmware and do the eprom fix etc. Should version 8 work OK with Arduino Mega versions.
Phil
I tried version 8.03, 8.05 and 8.11. All had the same effect.