I am having the same issue with payment modules after upgrading from v137 to v139h.
The modules are listed in Catalog > Modules > Payment. Shipping Zones have been defined.

These modules are present with red dots.
Authorize.net
Authorize.net
Authorize.net - eCheck
Ceon Manual Card v2.0.0
Cash on Delivery cod
The Zen Cart FREE CHARGE CARD
FirstData/Linkpoint/YourPay API
Check/Money Order

The option to install the modules is not present. Check/Money Order cannot be enabled either.
I installed the Ceon module hoping it would solve the problem but there is still no option to install.
In addition, this message is also generated at checkout;

Sorry, we are not accepting payments from your region at this time.

Any suggestions?
Thanks,
Michael