So coming back to this - the issue was third party optics which purchasing thought was officially Juniper, but in reality they were not. I believe the third party optics had some sort of issue with multiplexing on OM3. Official Juniper QSFPs stopped the port flapping. Configurations were all correct, it was definitely a hardware problem.
We have had issues with a couple Juniper QSFPs being dead on arrival, but that was relatively easy to suss out using:
request virtual-chassis vc-port diagnostics optics member # (effected member here) vcp-#/#/# (where this is the vcp port)
So for vcp-255/2/53 on member 4 it'd be like so:
request virtual-chassis vc-port diagnostics optics member 4 vcp-255/2/53
Then the following displays results:
show virtual-chassis vc-port diagnostics optics member 4 vcp-255/2/53
Key things I've found to look at are TX and RX signal levels and power. These are indicative of either a cabling problem, or if the cable is good it's likely a hardware issue if the signal and power is out of range.
Hope that helps anybody else beating their face on their desk about this.