adobe flash would constantly refuse to update when I ran an external SSD carbon copied from a pretty much factory fresh internal HDD
Disk util, command line checks, even an over install failed to find anything needing modified and all gave it a clean bill of health, yet problem persisted.
I ended up doing a complete install on it (boot to installer, erased the externals drive partition then installed to the empty partition)
Since then its been no bother at all
Anecdotal I know (and to be fair it was no great hardship for me as the flash installer issue cropped up and was spotted pretty early on before I started throwing major apps, document folders etc over to it)
Never encountered this previously when carbon copying 10.6/10.8/10.9 on the mac pros - just under 10.11 on this latest iMac
