Cruis AIO pro & multiwii 2.4
All props going in the right direction and ESC calibrated.
System armed, motors spin immediately (no problems there).
Test flight OK.
Added some switch behaviour through the GUI (matched to the appropriate code), clicked on WRITE, all OK
Went to arm the motors, GUI showed ARMED, lights on board showed ARMED, motors only started at 3/4 throttle position.

Only way to get it to work was with EEPROM clear and reinstall sketch. If I write to EEPROM same thing happens?
Any ideas, many thanks