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I don't think it's a timeout issue, I've seen scans over slow WANs take 4 hours to complete with no timeout. The scan will run to completion as long as there is data moving. Any time I see this type of issue it turns out to be a device or network config setting causing the issue. It's always difficult to to pinpoint the issue. Your test would indicate your network or a device (router, VPN, WAN optimizer) can't handle the traffic generated by scans of more than 1 or 2 machine simultaneously.
What are the specs of the servers running Protect? CPU - RAM etc.
How large are these groups? (possible IP addresses)
How are the Machine Groups setup? Machine Name? IP Range?
Are these mostly LAN or WAN machines?
Is the network known to be over-saturated?
What type of latency do you see when you copy a large file to once of the target machines? ping -t helps measure this.
Do you go through any WAN accelerators? Or any other device that would hijack the packets like a VPN?