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Sorted!. See https://forums.linuxmint.com/viewtopic.php?p=2644176#p2644176
But in a nutshell:
Get the proper value for StartupWMClass by running in a terminal xprop WM_CLASS,
the pointer changes, you click on an open window of your misbehaving application, i.e. for thunderbird esr via apt:

Code: Select all
user@machine:$ xprop WM_CLASS
WM_CLASS(STRING) = "Mail", "thunderbird-esr"
user@machine:
$ _

Use the second value, here:
Code: Select all
Exec=thunderbird %u
StartupWMClass=thunderbird-esr
Close all open application windows and save your .desktop file.

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Answer selected by tonywhelan
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