I would check system level logs to start like dmesg and syslog.
Someone else might have better tips of what to grep for in the logs. One thing you could do is try to ssh into the system when it’s locked up and check the logs to see what’s being reported during or immediately before the lockup.
Once you get a sense for what’s going on at a system level you can start to look in more specific logs.
Not to be that guy but have you checked the system logs when this happens?
I’d investigate the differences between the installs particularly around graphics and power management. It sounds like your system is getting woken up but it’s hanging at some stage in the process of resuming. You might get lucky and the issue might show up in the logs if you’re willing to investigate them.
When I’ve run NUCs in the past I’ve had issues with external nvidia GPUs dropping off the bus when resuming from suspend. To “fix” the issue, I ended up limiting the power state to S2 or S3 so that the graphics card was kept on the bus.
Do you know what display server, DE, power management service you were running on both? If the logs don’t turn anything up you can always compare the configs too to see how they’re suspending/waking the system.
Providing more specific information about what isn’t working would help resolve the issue.
The flathub page lists some additional steps that need to be performed to allow virtual input. Did you do this?