Anyone know why the Autoapply checkbox is disabled when accepting a payment?

That's just the default. I think you can auto-check that with SuiteScript.

try changing the amount to more than $0.

Tried that and same result

I thought that once you checked or uncheck the Auto Apply box on a payment and save it, the box retains the setting the next time you enter a payment. Check box is defaulting to checked in our account.