Just "voluntarily" upgraded from Powerdraft CE 14 to full Microstation CE 16.1 with a clean install (made all user settings from scratch) on latest Windows 10 and still running into the same problem:
When pressing on the file cleanup button the tool window doesn't show. I have a key assigned to "mdl load cleanup;cleanup do;cleanup window close" which works but it always says no duplicates were erased. The window shows for a fraction of a second the first time I execute this command and then won't show again. So I can't check if the settings are correct.
I also installed Microstation v8i SS10 and when doing the file cleanup in my current file it finds more than 2.000 duplicates vs. nothing in CE. Same behaviour in DGNs and DWGs.
What's going wrong here? Had the same behaviour in Powerdraft CE 14 before, so it might be a general setting.
Well, why did I write this before trying out something else first... Just created a new empty drawing and tested the behaviour there and found out it worked, the settings window opened. Now it also works in my "old" file.
Maybe it's got something to do with file settings made in older versions or from old seed files.
EDIT: Actually it only works once within the same file session. After hitting my shortcut it won't open in any file opened from within that Microstatino session unless I restart Microstation. That's quite strange, isn't it?
Have noticed also that some duplicates are not found in connect(Defect 1127069)