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I had a similar issue and it turned out to be an issue caused by Symantec Endpoint Protection and Symantec Backup Exec. The installation of these products in a certain order caused a registry entry that slowed everything to a crawl. The key to the slowdown was the registry entry, so you may have the same problem even if you don't have the Symantec products. See the following Symantec artricle:
As soon as I deleted the CLASS value everything returned to normal.
I had the exact same issue, and fought with it for a few months to no avail. I ended up completely re-installing the console on a new server and it has, at least temporarily, not given me any issues as of yet.
I tried disabling Symantec on the problem targets and that did not help. I wonder if I should have also deleted the CLASS value? Oh well...
After much tearing of (rapidly thining) hair I reinstalled the server and it is faster, though some individual machines take an age to scan.
I really wish I didn't have to manually type all the machine names and set up the Favourites after a reinstall - that must be REALY painful for those with many hundreds of machines. There must be a way to export these settings but I have never found that option.