The OP and myself have been back and forth about this functionality in my own forums and after some testing, I think I can clear up a few things for the OP, and assist in helping the author fix the bug....
OP is using a importing a .REG file on clean systems with his preconfigured settings from PatchMyPC on the original machine. The reg file sets the settings to skip certain apps and a few other bits... Regfile as follows:
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\Software\Patch My PC\Options]
"RemoveIcons"="1"
"AutoRunWindowsUpdates"="1"
"KillPrograms"="1"
"SkipMozillaFirefox"="1"
"SkipAppleQuicktime"="1"
"SkipAppleiTunes"="1"
"SkipSkype"="1"
"SkipMicrosoftSilverlight"="1"
"SkipGoogleChrome"="1"
"MinimizeToTray"="1"
"MinimizeToTrayUpdates"="1"
"RestorePoint"="1"
"Language"="English"
PatchMyPC.exe is being run with the /auto /s /update parameters.
The issue is that PatchMyPC appears as an icon in the system tray seemingly ignoring the /s, and it doesn't actually DO anything but sit there until you close it. If you open the app and click on a few action items, it will spit out an error message that something cannot be used with the /auto switch, THEN and only THEN will it start to work.
I've noted that if I remove the skip apps settings, and a few other things and pare it down to this:
Windows Registry Editor Version 5.00
[-HKEY_LOCAL_MACHINE\SOFTWARE\Patch My PC]
[HKEY_LOCAL_MACHINE\SOFTWARE\Patch My PC\Options]
"RemoveIcons"="1"
"KillPrograms"="1"
"RestorePoint"="1"
Then it actually works as intended. I haven't done further experimentation to see exactly WHICH setting is causing the trouble. It may be the skip <app> settings, or it may also be the minimize settings, or maybe the autorunwindowsupdate setting (which is redundant as I see when using the /update parameter, please correct me if I'm wrong...)
EDIT: Actually I just tried it with the skip <apps> settings and it appears to be working as intended. So it must be either the minimize settings or the autorunwindows update settings, which as stated appears to be redundant with the /update parameter - perhaps this could be the issue? Either way, I'm sure this issue is resolved enough for the OP to do what he intended.
I'm pretty sure we can work around these issues utilizing my above reg file, if that is acceptable to the OP... but non-the-less it appears a bug is causing the hangup somewhere that the author may want to investigate.
Hope this helps.