It's an old problem. This problem was solved but now appears again.

Are you on Wayland or X11?

Does the Meta+D shortcut work to show the desktop?

(In reply to Nate Graham from comment #2)
> Are you on Wayland or X11?
> 

X11

> Does the Meta+D shortcut work to show the desktop?

Yes

Is the `kglobalaccel5` process running?

(In reply to Nate Graham from comment #4)
> Is the `kglobalaccel5` process running?

yes

Can you attach your ~/.config/kglobalshortcutsrc file?

Also can you paste the output of `ls ~/.local/share/applications/`?

Created attachment 150821 [details]
kglobalshortcutsrc file

x@grincheux:~> ls ~/.local/share/applications/
Android.desktop                                          org.kde.dolphinsu.desktop
Captvty_2.desktop                                        SNCF - TER m Nouvelle Aquitaine.desktop
Captvty 3 a-2.desktop                                    userapp-Thunderbird-5N6AB1.desktop
Captvty 3 a.desktop                                      userapp-Thunderbird-IQF7A1.desktop
Captvty (captvty_v2).desktop                             userapp-Thunderbird-W4KJB1.desktop
Captvty.desktop                                          vlc-2.desktop
chrome-aghbiahbpaijignceidepookljebhfak-Default.desktop  vlc-3.desktop
chrome-agimnkijcaahngcdmfeangaknmldooml-Default.desktop  vlc-4.desktop
chrome-bkaeedcadgimgkieaecleinibbmmohfd-Default.desktop  vlc-5.desktop
chrome-ccfhmamjfjjngdoaghgfjljhbfekiaea-Default.desktop  vlc-6.desktop
chrome-celnaknmndcdcjcagffhbhciignkeokb-Default.desktop  wine-extension-application.desktop
chrome-dhdicmjdheacodbikpgdnpoehpinnkcf-Default.desktop  wine-extension-appref-ms.desktop
chrome-eilembjdkfgodjkcjnpgpaenohkicgjd-Default.desktop  wine-extension-chm.desktop
chrome-fmgjjmmmlfnkbppncabfkddbjimcfncm-Default.desktop  wine-extension-compositefont.desktop
chrome-fnpcjaogcceklblplhgnpbfniinngckj-Default.desktop  wine-extension-crd.desktop
chrome-hnpfjngllnobngcgfapefoaidbinmjnm-Default.desktop  wine-extension-crds.desktop
chrome-hpfldicfbfomlpcikngkocigghgafkph-Default.desktop  wine-extension-gif.desktop
chrome-imgohncinckhbblnlmaedahepnnpmdma-Default.desktop  wine-extension-hlp.desktop
chrome-jgeocpdicgmkeemopbanhokmhcgcflmi-Default.desktop  wine-extension-htm.desktop
chrome-kjbdgfilnfhdoflbpgamdcdgpehopbep-Default.desktop  wine-extension-html.desktop
chrome-lalmblomncladncgkgmobohkgmhdnnch-Default.desktop  wine-extension-ini.desktop
chrome-maonlnecdeecdljpahhnnlmhbmalehlm-Default.desktop  wine-extension-jfif.desktop
chrome-mnkilndbacbepalimifanofdpoibbjjo-Default.desktop  wine-extension-jpe.desktop
chrome-ncmjhecbjeaamljdfahankockkkdmedg-Default.desktop  wine-extension-msp.desktop
chrome-oddpdajgokdcmlogaiagaogocojnomcl-Default.desktop  wine-extension-pdf.desktop
chrome-oojinfmcohjejmjaaeefikpgdghbooim-Default.desktop  wine-extension-png.desktop
chrome-pfjkjfejkdjepkfkiabgkmdjemejcfok-Default.desktop  wine-extension-pyw.desktop
chrome-phladhlohklpjnppempdiepflgkfpcdn-Default.desktop  wine-extension-pyz.desktop
chrome-pmcngklofgngifnoceehmchjlildnhkj-Default.desktop  wine-extension-pyzw.desktop
Clight-Gui.desktop                                       wine-extension-rtf.desktop
kglobalaccelrc                                           wine-extension-txt.desktop
Kindle.desktop                                           wine-extension-url.desktop
Kobo.desktop                                             wine-extension-vbs.desktop
konsolesu.desktop                                        wine-extension-wri.desktop
mimeapps.list                                            wine-extension-xaml.desktop
mimeinfo.cache                                           wine-extension-xbap.desktop
org.kde.digikam-2.desktop                                wine-extension-xml.desktop
org.kde.digikam.desktop                                  wine-extension-xsl.desktop
x@grincheux:~>

I see:

[.desktop]
_k_friendly_name=Captvty_2
_launch=Alt+R,none,Lancer Captvty_2

I wonder if the Alt-key-based shortcut interfering with the alt-key-based mnemonic system. Does this shortcut work if you change the key combination to something more likely to be unique, such as Meta+Ctrl+R?

Meta+Ctrl+R does not work

Darn. I don't know what it might be, then. Hopefully a more skilled developer than me will show up and help figure it out.

I deleted all my failing custom shortcuts created with kde menu editor or kde settings > shortcuts >  shortcuts
I created with a third method my custom shorcuts : kde settings > shortcuts > custom shortcuts > edition > new > global keyboard shortcut > command/url

All this custom shortcuts runs again with success .

It is less handy because I must copy the launching command from kde menu editor and  paste it in the command field of this third editor.

The question is: why suddenly a part of my old custom shortcuts fails ?

I made this hypothesis.

All app launched with a failing custom shortcut get a kde menu launcher but are not actual app :
- youtube is a Chrome web app with launching command "/opt/google/chrome/google-chrome --profile-directory=Default --app-id=agimnkijcaahgcdmfeangaknmldooml"
- captvty_2 is a wine app with launching command "/usr/share/playonlinux/playonlinux --run "Captvty (captvty_v2)" %F"
- vlc_2 is a script with launching command "/home/roubach/bin/vlccl.sh"

No problem with the shortcut of digikam which is an actual app.

I can add a shortcut to a non-KDE app, or use some of the existing shortcuts, but there is no way to add or use a shortcut to Kate.

I think this is related to bug 456589 — at least in my case…

For many years kde got a problem with shortcut !

As a workaround, for entries I use all the time, I created new .desktop files with no "options" in them (because the options are not really needed or I call an intermediate shell script).

(In reply to Michel from comment #17)
> As a workaround, for entries I use all the time, I created new .desktop
> files with no "options" in them (because the options are not really needed
> or I call an intermediate shell script).

If i understand well
as I said in the comment #11

I created with a third method my custom shorcuts : kde settings > shortcuts > custom shortcuts > edition > new > global keyboard shortcut > command/url

No need to create desktop file or script.

*** This bug has been marked as a duplicate of bug 440507 ***