I have a similar problem as well. Two Servers, Same Version.
Now, I have a New Server with Windows 2008 64-Bit Server with Backup Exec v12.5 w/SP1 64-bit.
On the Old Server (BE v11 7170 SP4), I copy the selection list over to the New Server.
Works if the Selection List is Exchange 2003. But does not work for Flat Files, SQL, or Sharepoint. And Symantec Support was not able to answer this. Just a BIG...question mark....on everyone's head.
I've found the problem!
After SEVERAL TESTS....this is what I've found.
If the Selection List has more than 15 servers to be backed up, you cannot copy the selection list to other media server or from v11 to v12.5 Backup Exec Server. But you can copy the selection list to the same media server (local) no problem.
If the Selection List has 15 or less Servers to be backed, you can copy the selection list to other media servers and from v11 to 12.5 Backup Exec Server.
This is obviously A BUG in Symantec's Backup Exec.
Called Tech Support regarding this issue...
Apparently, the problem is in the View Details of the Backup Selections. If the number of lines in the Details is too much...it will timeout.