Same issue for even a single Git SCM entry. The high-level config.xml nodes for the Git SCM plug-in are created, though they don't actually take data from the web UI – so they're all just defaults/blank, and the actual XML node that would contain the repo list is missing altogether. I suspect the Multiple SCM plug-in is not handling the repeatable sections properly, or the actual web UI is broken. This in turn could be due to an issue with the git plug-in rather than Multiple SCM. See my previous comment regarding this.
You can at least hack the config for a Job, in order to get it to work with Git SCM entries. This doesn't solve the problem of viewing/editing the config, but it does allow builds with multiple git repos, which proves that in theory this could work.
I started with one GitHub SCM entry, created with Multiple SCM's UI. I left it blank when saving, because it won't do any good to fill in details anyway. I then edited ~/.jenkins/jobs/MyJob/config.xml as follows (i.e. specifying a dummy repo here called email@example.com:foo/bar with a working directory of test_1), and restarted Jenkins:
Note that originally everything between the <configVersion> and <recursiveSubmodules> nodes was missing, and I copied the <remoteRepositories>, <branches>, and <mergeOptions> nodes from another Job that had a single Git SCM (without Multiple SCM). Also, evidently the <relativeTargetDir> node wasn't being saved either (amongst possibly other options), so I put this in.
After I verified that the build/clone worked, I then copied the whole <hudson.plugins.git.GitSCM> node as required for additional Git entries. Again, after a restart of Jenkins, I was able to run the build with multiple git clones.
While this still doesn't seem to show the config when you're editing the Job, it does appear to do the git clone when you build the Job.