Hi Ben.
The device concerned is PIC32MZ2048EFG144, and no bootloader.
It's a bit of a handful, and we're progressively getting to know it better, though appears to set itself apart in the way you have to configure and use it. Other things seem not to make sense, such as growing silicon errata (the 'fix' for primary and secondary oscillators, not working as crystal clocks, being not to use them was amusing), and configured/enabled ADC's still returning noise (still investigating that). One of the ICSP pins was also mapped as UART RxD but refused to work as such, so we moved it and all was well.
To resolve the flow control issue it was a matter of using the specified pins for the chosen UART block, and affirming flow control pin selections in FC7. I don't believe we attempted to preset registers to disable hardware flow control as we'd expected the choice to be arbitrarily selectable (as per your separate post), until we discovered this behaviour.
Of-course I'm unable to rule out pin-specific weirdness and bad luck in choice (similar to the RxD issue above), though I'd generally recommend anyone using flow control on the PIC32MZ to stick with pins designated by datasheet when using hardware blocks if they can to minimise potential for issues.
Probably just the hallmarks of early silicon, unless you should highlight an oversight Ben
Best regards,
Brendan