For RB1200 rebooting you need to write to support and get pre-production v5.10 with the fix.
For all port flappers - each Ethernet link have 2 ends and a wire in the middle, so 3 potential points of failure or simple incompatibility between 2 devices.
AFAIK port linking is a hardware feature and as WirelessRuby explained, only thing new in software was log messages.
I have seen port flapping for many different reasons:
- old Cisco devices didn’t talk normally to other devices
- not shielded Ethernet cable near high voltage power lines
- shielded, but not grounded Ethernet cables
- Partially blown Ethernets on boards, because of lack of grounding
- some POE injector problems
- too long or too short Ethernet cable
So from where i stand - all those “I upgraded and my ports started to flap” problems makes me smile. “yea, right!”