Hi,
I'll try to guess what's happening on the WFE side. Set the DPM logs to verbose on the WFE, restart the agent, launch a catalog creation on DPM PowerShell, and look at the CmdletWrappersCurrent.log file in the WFE, where the agent goes contentdb by contentdb
creating the catalogs (it is quite verbose as it gives a lot of detail). This way you can get to know whether the indexaton it is simply very slow or if the agent is stuck somewhere. do you have many content databases?
If you have a large farm with a very big number of items, then the problem could be in the DPM database. You should reorganize/recreate indexes on the table that stores the catalog:
http://technet.microsoft.com/en-us/library/ff399024.aspx
HTH
Roberto