Have you tried portmaster instead of portupgrade? I've been using portupgrade all along, but I'm finally switching to portmaster because it is evidently better supported these days.
Have you tried maintaining your PHP ports by using cd to go to the relevant port directory, then doing a "make install clean" directly from there, and otherwise doing it more "manually"? I wonder if there's something particular to portupgrade here, though it should be the opposite really -- portupgrade should handle the whole process better. It's just worth considering.
Do you check the /usr/ports/UPDATING file before doing any upgrades? If there are special instructions that need carrying out for a port when upgrading it, they should be listed in there. If you aren't checking that already, I'm about 98% sure that starting to check that will solve most if not all of your problems -- though take it for what it's worth, because I don't deal with PHP on FreeBSD (or anywhere else, these days, if I can help it) at all.
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