That is quite surprising. What version of the git plugin are you using?

There was a known problem in git plugin 2.4.3 (fixed in 2.4.4) which caused it to fail to preserve the configuration across saves (and Jenkins server restarts). It might have also shown as a failure to save configuration across upgrade. See JENKINS-33695 and JENKINS-33564 for the descriptions of that bug.

We're on 2.4.4 at present. It looks like the git module was updated along with jenkins so I'm assuming this was a result of the 2.4.3 bug then ?

The 2.4.3 version of the plugin was only available for about 7 days (19 Mar 2016 - 24 Mar 2016) before it was superseded by the 2.4.4 version. I would be surprised if you were running 2.4.3, since it was replaced over two months ago by 2.4.4.

You should be able to see check enough of the plugin installation history from your "Manage Plugins" section called "Installed Plugins". If git plugin 2.4.3 was on your system prior to 2.4.4, it will be listed with a large button "Downgrade to 2.4.3" on the line for the git plugin.

If the version number in the "Downgrade to " button is not 2.4.3 (possibly 2.4.2 or 2.4.1 or 2.4.0), then you probably never had 2.4.3 on your Jenkins server.

If you never had 2.4.3 on your machine, then I don't have any good suggestions for the cause of the problem you're seeing.

Are there specific additional behaviors which are not preserved, or is it all additional behaviors that are not preserved?

The downgrade button is offering 2.4.3 so that looks like the culprit. We've hit on this issue previously when updating / restarting jenkins so I'm guessing we've had 2.4.3 for some time and only just bumped up to 2.4.4.

AFAIK checkout to sub directory and possibly git sub-module behaviour was impacted. I don't know if we're using anything else.

JENKINS-33695 and JENKINS-33564 both are duplicates of this bug