Well done for circumnavigating the issue by swapping out the top ends. As you say, there's something wrong with that top end, whatever it may be. They tend to be very soft and wear out as quickly as they are run in so not really viable as a long term option.
Whilst the inlet duration quoted shouldn't have been an issue, I wonder whether if the position / relationship of the ports is causing issue, allowing too much communication overlap? Also, some postons have a steeper angled side than others (imagine the side angle of a thimble), with the original SR pistons being rumoured to have been questionable. If the side angle is steep then the cutting short could leave excessive clearance to the piston, causing rocking and slap... although rings should be stopping excessive blow-by, if suitably gapped.
^... probably enough of your time wasted on that cylinder though!
Thanks for letting us know.