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It does not matter, what happens *after* IPrefs is loaded. The error occurs *before* IPrefs. As the message says, IPrefs tries to close the Workbench screen but there are some windows open which prevent the screen from closing. So check which windows are open and correct the programs which opened them. The usual windows are the initial CLI window which opens if a program in startup-sequence or user-startup writes some text to the console (e.g. an error or copyright message) or a requester telling you that there is a problem e.g. with the CD-ROM drive. The latter is usually hidden behind the IPrefs requester.
If you know which program causes windows to be opened, it's easy to correct: either remove the program, add >NIL: to the command line or correct the CD-ROM mountlist.
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