Strange.
I didn't know about hese .desktop files but looking for them finds
them not only at the same place in the directory tree, but with the
same date as my home-compiled /usr/local/bin/vim binary (to which
/usr/local/bin/gvim is a soft link). Comparing them with vimdiff shows
that they are extremely similar, though not identical, to each other.
Most of the differences are what one would expect from .desktop files
meant, the one for gvim and the other for vim.
Normally I start Vim either as "gvim -S" with a handwritten session
file from a handwritten desktop icon, or by typing the executable name
(vim, view, vimdiff, etc.) with apropriate arguments at a bash shell
prompt, thus entirely bypassing those .desktop shortcuts (which are
not installed on my KDE desktop anyway). This never gives me problems.
I am on openSUSE 15.1 where I compile and install the latest Vim
(currently 8.1.1933) every time I see a new version on Christian's
Mercurial mirror (presently the
256bit.org one, in prevision of
Bitbucket's demise as a Mercurial hosting facility in a little less
than a year) of Bram's master repository on github; my other software
packages come from the openSUSE 15.1 distro's various software
repositories, including the "Update-Test" repository; for instance the
Linux kernel there is at version 4.12.14-lp151.28.3 where the part
after the dash is a kind of "SUSE build number".
Best regards,
Tony.