43 or 26 megs - it is nothing. That can happen that some cache is filled in HE which runs for a while or you have a lot of stuff in Undo.
It is not really easy to say what is a reason for such slowing down. I would not say it is a memory. I seen such effect for very long lines, but in that case it 100% reproducible.
Probably some linear search/check, which was not caught (because of the some specific parameters).
I need to be able to reproduce it to get it. The only thing which can help here, is putting aside HE pdbs and try to run some profiler to see which functions consumes most.
If delays would be longer than several seconds, you can use Process Explorer, which shows call stack for a process too.