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The first thing - what version of Protect are you running, and what are the specs of the Protect console system (processor, memory, etc.)?
This document could prove helpful:
The logging for Protect would probably prove to be the most helpful in determining which system(s) are being scanned when the slow down occurs, however, there would be a lot to look through and you'll need to contact support directly so we can provide you a tool that can be used to allow multiple scan logs to be saved since this scan might be too large to be completely stored in the logs based on the default settings (even when set to All logging).
You can create a case direct with support at https://support.shavlik.com/, and please reference this discussion.
We have the same issue at the library, found that a location is connected to the network via VPN even though it is only 6 machines it takes up to 3 hours.
Generally when I've heard of something like this, there is a high latency in the connection between the console system and the target system(s). That would be the first thing I'd suggest checking for. There's not much you can do about it if there is a high latency (unless of course you can improve network connectivity) - this will basically cause the scan process to take much longer. However, the best workaround is to install a Shavlik Protect Agent on the systems where you see higher latency. That way the actual scan process takes place on the system itself instead of going over network traffic.
Hope that helps. If you still can't figure anything out after going through this and the things I mentioned earlier it might be a good time to open a case. Shavlik Customer Support Portal
Sorry for not updating this post sooner but I did in fact put in a suppot request a few weeks ago. They check the log files and did find that several clients were having unusually high timeouts. Right now we're testing setting up a group of only IP based machines (I have it set up by OU now) and see if that helps at all. Not an idea situation at all though, as we name our computers by location so it makes it easier to see what branch they belong to. I'll update again when we find something more concrete.
Oh, and our slowest circuit is 100mb so latency is most likely not the culprit. I won't rule it out though, there's always the possibility of a port speed mis-match somewhere.