What do you think about writing this as a windows service?
I currently run AmpCtrl (it runs as a windows service) and all it does it turn my amps on when windows loads, and off before windows shutsdown. This completely stops the turn on/off pops. Only bad thing is that AmpCtrl uses my only DB-9 serial port. (Yes, I know you can use USB->serial adapters)
If this app were a windows service, then it could could tell the DS-ATX when to turn on the AMP-ON pin on the DS-atx board. That would remove the need for AmpCtrl, and then also allow you to have an awesome GUI control for the DS-ATX.
Jeff (zootjeff - the DS-ATX maker) might also be interested in helping, as this would give his product a huge increase in features, as you would now be able to implement a LOT of features in software to control the current DS-ATX state and timers,.
Id also like to get my DS-Atx using USB. Either via a serial->USB adapter, or a different MAXim chip (if there is that kinda thing).
Peace