mythtv_setup.pl does not observe db string length restrictions
The storagegroup table has a restriction of 32 chars for groupname. This is exceeded if you use the default LMCE names for shares, eg here is a line from the storagegroup table:
| 116 | public: Windows Share-public [| localhost | /home/public/data/pvr/Windows Share-public 193 |
You can see the name has been truncated. This means that when the script is run again it reports the entries are not present, as it is looking for the full groupname, not the truncated version.