Since quite a while I was thinking of writing this but have always postponed till now...
So there it goes:
My observation is that mostly I need to use alternate fingerings when reaching for the troubling notes on C trumpet (such as 2 ledger line E and E flat, sometimes D and very occasionally C) when playing ascending intervals leading to the mentioned notes and eventually when it is a starting note.
Apparently when coming down from higher notes to the "troublesome" notes seems to sound mostly in tune.
Anybody else having similar observations?