Hmm. Looks odd. We have around 60k tiles in archive and it does not show any problems neither on load, nor on merge.
Does this happen instantly when you start the tool or when you press Map Merge?
The program does not load sessions on start so a number of proccessed but not deleted sessions' folders can't be the issue, they will only increase time for the next map merge.
And it must cache tiles that are visible on the screen only.
Anyway, I will see what can cause such problems and will wite you back later today.
Could you please test the previous version meanwhile? It is still available for download. It would be helpful to know if it causes the same problems or not.
Thank you for the feedback. Lets make it better together.