Running PM on Windows 10 64 bit, PM is Version 4.81.1154 and IERenderer is 2.7.1.3.
Seem to have a problem with the listing of open windows (or panes) (see image ) - I normally have PM in 'Preview' mode and when I start a new message it appears on top of the 'Folders - New mail' window and any other window (pane) will be listed at the bottom of the 'Window' menu items.
However, of late, only '1 Folders - New mail' is listed at the bottom of the 'Windows' item list, no other windows listed.
If I minimize the 'Folder - New mail' pane, the other windows are behind it.

I have never seen this.
Restart Pegasus Mail if you haven't.
If that doesn't fix it try a restart of the PC.

If you routinely use the Window menu item I wonder if you know about the Window bar that shows open windows in a tab-like bar along the bottom of the main window. It can be toggled on/off by clicking the blue triangle located bottom right.

Restarted PC and then PM - same behaviour.
I hadn't really noticed the Window bar, but I can use that instead of the Window menu.
I'll likely leave things as they are and maybe do a new install when the new version comes out and move messages over to the new install.

Well, I've resolved the window (pane) problem, but in a roundabout way.
I usually keep a backup of messages on a laptop and copy over everything in \PMAIL\MAIL\ADMIN except PMAIL.INI, STATE.PMJ, and HIERARCH.PM.
The laptop did not exhibit the window (pane) problem, but was at PM v4.80.1028 and IERenderer v2.6.6.0
So I did my usual copy to the laptop and, in steps, updated PM on the laptop to IERenderer 2.7.1.3 (no window (pane) problem) and then to PM v4.81.1154 (no window (pane) problem).
Copied the complete \PMAIL folder (directory) from the laptop to the desktop, and it all works as it should with no window (pane) problem.

Nicely done. Thanks for reporting back.

If I understand what you did correctly, the end result was that PMAIL.INI, STATE.PMJ, and HIERARCH.PM where the only configuration files replaced on the desktop PC with the ones from the laptop. I'm sure the problem wasn't in HIERARCH but am clueless how PMAIL.INI or STATE.PMJ could have caused your Window menu issue. The question then is whether a corrupted program file was causing the problem. Beats me! I'm glad that you found a fix.