I have sent you email and PM requesting your private email address, in order that I can send you a special test version of pbedit.exe as email attachment.
When you get the test pbedit.exe, I would like you to:
-- Launch pbedit.exe, and load up your scenario.
-- Do the hotkey combo Ctrl+Alt+5.  This will raise your so-called "LogLevel" from the default 1 to the new higher level, 5.  You should see a pop-up like this:
 PzBOnLogLevel1.JPG
  PzBOnLogLevel1.JPG (Size: 258 KB / Downloads: 4)
-- Add units (or whatever).  Note that at LogLevel 5, very many entries are added to Logs/pbedit.log.  This in itself will slow the program down, with so very many disk writes.
-- Be patient.  Both the heightened logging and the issue you describe will slow you down.
-- When your editing session slows down, perhaps "freezes", wait a while, 5 minutes say.  Then try doing something, maybe add another unit.
-- When you can no longer stand the slowness, 
without shutting down (exiting) the editor, leaving it as is, zip up the Logs/pbedit.log file, and post it here.  It is important that you not quit the program unless/until you have prepared (and posted) a Logs/pbedit.log file (zipped) that shows activity at the time of the slowdown/freeze, not before, not after (after exiting the editor).
The pbedit.log file might be quite large.  But after zipping it up, it should be a manageable size, suitable for posting (or perhaps emailing).
Depending on what your initial pbedit.log shows, we might need to do this exchange -- me sending you customized pbedit.exe, you sending back zipped pbedit.log -- again, and maybe again.
We'll see how it goes.  Good luck.