Where, exactly, are you seeing "server IPL required"?
On an individual PTF when looking at 1. General information?
On the list of ptf's when looking at the column "IPL Action"?
DSPPTF OUTPUT(*OUTFILE) OUTFILE(QTEMP/DSPPTF)
sql that and delete the ones which are permanently applied. Then start
your analysis from there.
Other things which will affect PTF application include if your IPL was
'abnormal'. WRKSYSVAL QABNORMSW.
Sometimes you may have PTF's that are missing coreqs or prereqs. See GO
LICPGM, 50. Display log for messages. You may have to delve into the
joblogs for SCPF, active and past. If it's been too long since your last
IPL you may be missing this history. GO CLEANUP will clear it out after
the number of days you tell it to.
Also, look closely at those PTF save files. Are some PRIOR to V5R4? If
so, and you failed to apply them permanently before upgrading to V5R4 they
will remain there for all eternity. Years ago I started applying all PTFs
permanently (along with an extra IPL or two) before upgrading my OS. This
helped prevent new ones from being left over. The older ones I had to
manually delete. I think I even discovered some V2 PTFs.
Oops look at the time. This may be chopped - gotta go.