I've made a CAPsMAN setup, but there is one flaw in it. When I boot in CAPs mode with the reset button after a power outage it won't boot back in CAP mode. Is there a way around this?

You do not provide any relevant information to TRY to help you.

Exactly what relevant information do you need to answer the question?
Using routeros 6.40.2
CAP's: WAP AC

Please try to boot device in CAP mode after that generate supout file on router and send this file to support@mikrotik.com. Do you have only one such device?