I don’t think subnotebooks would make a difference. I’m not familiar with pCloud but one issue with filesystem sync is that it’s quite sensitive to the file timestamp, so if the tool you use somehow messes with or doesn’t transfer the timestamps correctly, it might affect sync.

What you can try is identify a note that’s not syncing in Joplin, and get its ID (in the Info dialog). Then check on the sync target if you can find this ID. Finally check its timestamps to see if there’s anything strange. Also check the log in the profile directory for possible errors.