FYI: I ran into this same issue on CentOS 6.5. Old directories had symlinks like:
lrwxrwxrwx. 1 jenkins jenkins 19 Apr 22 09:06 401 -> 2015-04-22_09-06-23
New directories looked like:
drwxr-xr-x. 2 jenkins jenkins 4096 Mar 1 01:28 317
The UI showed the old builds as having run before I was born! In order to re-run the migration I did the following:
sudo find /var/lib/jenkins/ -name legacyIds -delete
sudo service jenkins restart
Once this was done things looked correct.