My setup also uses JRiver Media Center 28 Service with Startup Type: automatic. This causes the MC 28 Server process to appear very early in the Windows startup cycle. Note the service is distinct from app Media Center 28 which is listed as a Background Process in task manager, and then moves to the App section once you open a GUI. Discovery has been very reliable for me. Typical discovery failures are when new Win 10 (Win 11) updates sit around in the background to be installed, or following an off-normal shutdown, such as a windows update reboot or reboot after a power failure. Then it may take an extra reboot to get back on track.
As you indicate, there could be some kind of blocking between MC 25 and MC 28 with regard to network discovery, or a startup time issue. If MC 25 started first, then the Marantz cached information about its network address, servers, etc. When MC 28 followed later, the Marantz may have been confused about who to respond to. The SSDP/UDP protocols should be able to handle this properly based on packet headers, but you never know about the various implementations. More generally I would think running multiple MC versions simultaneously is just asking for trouble.
In any case I'm glad to hear MC 28 is working with the Marantz.