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On a German keyboard layout I tried to assign "Ctrl + ä" to a custom command (here as an MWE the predefined command "Google Search"). As long as MC is open, it works. But if you close and restart it, the shortcut is gone.

The key binding is successfully saved to "CustomKeymappings.xml" as

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<map extid="" ctrl="0" udc="3146babb15934bc6b53872c1c6c1dfc9" key="OEM7" keymod="C"/>
but it is not properly loaded when MC is restarted. (See the attached picture)

The symptom seems to be the same as reported here:
http://forum.multicommander.com/forum/index.php/topic,836.msg2457.html#msg2457

I am suspicious of the VGA driver involvement in this as it appears more frequent on some AMD driver versions than on NVDA.  I do not have enough different hardware to test this suspicion fully tho

I think this is not related to any video driver issues since I have an Intel GPU (inside a CPU) and an nVIDIA GPU which both show the same behavior.

And Matthias already stated that this seems to be a bug in the window handler of Windows 10 1809.

i reported this already...... http://forum.multicommander.com/forum/index.php?topic=2666.msg9164#msg9164

I had seen your post, too. But this thread is older, and heading and description are more detailed. That's why I choose to post here, even though Matthias (Author) posted a more recent answer in your thread.

But I think, you have a good point. It's odd that the copy/move/delete dialog gets its own icon in the task bar and is not stacked above the "main" icon. Maybe this might really solve the problem.

I had this issue also for some time now and tried different things to find out where it came from without success. Then today I specifically installed Windows 1809 on my second machine—where the bug did not occur—just to test if the new Windows version was the problem. And: yes it was. After that I found this thread. 

I figured that it only happens if in the move/copy/delete dialog a message box is triggered where you have to choose an option. After you made the choice and the move/copy/delete dialog closes Multi Commander doesn't get the focus back but the last used window before Multi Commander gets it.

If you want to trigger the bug, delete a non-empty folder or try to delete a used file.

MC do not mess around with the registry it self..  But it asks windows about drive and volume. and Windows might go out and get that information.

You can try the latest beta and turn on full logging and check the app log at what stage it takes long time.

Thanks, for your tip. I enabled the debug logging and found out that the delay was during enumeration of the drive letters. Then I saw that my floppy drive was still active in the device manager even though I have disconnected it. The deactivation in the device manager resolved the delay.

For me the reading of the configuration during the start of the program also takes a few seconds. It happens on multiple different computers and it started some time ago.
The computers' age and hardware are different but all run Windows 10 Pro x64.

I tried to delete the configuration, but it didn't help. I tried the portable version, also some older ones (32bit and 64bit) with an empty configuration. And they all take this elongated time to start.

I don't use any special AV, just the Windows Defender. But deactivating it also doesn't help.

I tried using Windowse's Safe Mode, no change.

Here is some information about the "gap" I gathered using Sysinternal's ProcessMonitor:

Time of Day	Process Name	PID	Operation	Path	Result	Detail
23:32:45.6825275	MultiCommander.exe	788	RegCloseKey	HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\MountPoints2\CPC\Volume\{[GUID removed]}	SUCCESS
23:32:51.2647950	MultiCommander.exe	788	RegQueryKey	HKCU	SUCCESS	Query: HandleTags, HandleTags: 0x0

I did the logging multiple times and the gap is always between these two entries.