I am updating from 1.27.4 to 1.31.0 and have the same problem. @Ciencia Al Poder thank you for identifying the cache as causing this problem.
First, I confirm this is a cache problem. I can reproduce this problem using the Math extension as an example. All of my testing is on localhost.
In ($IP)/extensions, clone the extension from the git repository.
Install this new version:
#git clone https://gerrit.wikimedia.org/r/p/mediawiki/extensions/Math.git --branch wmf/1.32.0-wmf.14
My LocalSettings.php has:
$wgMainCacheType = CACHE_MEMCACHED; #memcached
The reported Special:Version of 3.0.0 (20f8d16) 12:39, 23 July 2018 is correct.
Install the 1.31.0 release:
#rm -rf Math/
#git clone https://gerrit.wikimedia.org/r/p/mediawiki/extensions/Math.git --branch REL1_31
Using the same LocalSettings.php as before (memcached), I refreshed my web browser to show:
The Special:Version reported version: 3.0.0 (20f8d16) 12:39, 23 July 2018 has not changed (not correct)
I then modified LocalSettings.php to disable the cache.
$wgMainCacheType = CACHE_NONE;
I refreshed by web browser to show:
The Special:Version reported version 3.0.0 (a1263db) 22:54, 16 April 2018 (correct)
Changing nothing but LocalSettings.php to (enable memcached) or (use no cache), the reported version follows the cache (incorrect when used), correct version is shown with no cache.
Inspection of the source code shows suggests a git API is extracting the status information in real-time. The variable $wgExtensionInfoMTime is for a different purpose as you suggest and does not fix this problem.
It is important to have the correct information when displaying this page. Is there a way to clear the cache (or disable the cache) for Special:Version?