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I hit this too. I got past it by doing the following:
1. realized command line git was missing on the Jenkins box, so installed it (e.g. yum install git)
2. installed the scm-api Jenkins plugin (I am behind a firewall and have to manually upload each plugin).
3. restarted Jenkins
I am pretty sure it was the first line item that caused this issue, but I included #2 just in case not. Make sure to look at the system logs (Manage Jenkins->System Logs) as I found them to be helpful in diagnosing the root cause. Also, restart Jenkins whenever you want to retest it - it seems to help.
As a pre-flight test, you should be able to do this on your Jenkins box:
1. ssh [your host]
2. sudo su jenkins
(you probably need to update /etc/passwd to give the jenkins user a valid shell before this works)
3. cd
4. mkdir test
5. cd test
6. git clone {the repo URL}
If #6 fails, then you have some work to do before looking deeply at SCM Sync.
@stunney it looks like you confirmed you had git command line installed, so it may not be the same problem.