I am having exact same problem, customer paid yet it doesn't credit the invoice.   I have yet to figure out how to get it to apply.  When I go into Merchant Services it just says forever . . .Please wait... we are matching your deposits to QB desktop records.   

and yes I have done all the updates, upgraded to Mfg & Wholesale 2022 so QB people don't ask me again my version.  I spent 35 min on chat and they did nothing but try and sell me Enterprise.