@Patrik
If you refer to the grey to white flashes, then yes!
Also, the power led should go from dim to lit.
If your the power led goes lit atleast the 68k is working otherwise it's dim.
I use a CyberVisionPPC GFX board so I usually don't see the flashes but changed the cable to the Amiga VGA connector and there whey where. Very fast althought.
There are still a few things to check if it doesn't power up. Is the fan on the PPC alright. If not it may draw to much power so the Amiga can't boot. Happened to me! Also, check the motherboard switches again. If they are wrong things won't work to well. CPU clock may have to be set to INTERNAL. Has to on A3000, otherwise the MB CPU fries.