It seems that a bad version of the g3tremb2 archive has been found in the MG repo. This version goes back years, and I suspect it originated from when the repo was originally set up.
I've obtained a copy from
TJW's Site which predates the MG repo and replaced the flawed version in the Repo with it. I've found that other repo's are using the same version that was in the MG repo, which I suspect is the source of the file.
This map name is g3tremb2
also known as Infested Pump Station
md5sum of TJW's version:
fc00367511f661ccd2a1963ce4ed191e g3tremb2.pk3
md5sum of MGs version:
979811158a943fa9b2484def76cca91c g3tremb2.pk3
The only difference I've been able to determine is that the MG version will not unzip correctly from the command line:
unzip -l g3tremb2.pk3
reports an invalid archive.
Here's where the real problem crops up.
If you have the bad version on your server, and someone downloads the correct version they will be kicked from your server since the md5sums don't match.
Additionally, if you're server has the correct version and someone's client has the bad version, they will be kicked when their client tries to load it since the md5sums don't match.
I don't have any definitive proof, but I'm pretty sure that this is directly my fault

It appears to go back to when the MG repo was set up, and many of the maps where copied from my server at the time which had every map I could get my grubby little hands on.
Very sorry for the headache I've caused, if any.