So to be 100% sure:
You're in that folder. The mouse cursor is not over any file at all. CTRL+A => XY "freezes" for about 25 seconds?
Correct, tried again with cursor on other monitor and same thing and yes, XY freezes with CTRL+A.
Also, tried on another directory that is about 900gb in size which has 902 sub-directories and files within and had no issues with cut and paste, so certain this is on large file selection only.
Did the fresh instance on XY again and no freezing with CTRL + A on those files.