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This sounds like one of two things.
It could be that your database is slow. Is the SBData folder on a local drive or is it on a NAS? Make sure the database is stored locally, on a fast drive. Also make sure that a backup or reporting job is not running during your deployment. Finally, if your environment is 5,000+ nodes, you should look into enabling indexing on your database. This basically entails putting a dbcfg.ini file at the root of SBDATA. The parameters are shown in the admin guide, but I'm sure support could send you one or walk you through the config.
It could also be that your network is slow. When customers report this issue it is almost always when they have a server in one country and users in a distant country. A common root cause here is a poor WAN link. Are the failing installs happening in a far away land? If not, this will become a general network troubleshooting exercise. Network problems can also occur if you have too many concurrent connections. We support 200 out of the box, but those can be quickly consumed if you are assigning a large number of users to each machine. It takes ~1 second for each user account to be pulled down to a machine during that initial sync. So if you are pulling down 1,500 users, then the sync will take 25 minutes to complete. That means connections will start to get dropped if you deploy to more than 200 machines in 25 minutes.
One final thing to check on the network side is the client firewall. I saw this once and the customer had the Windows firewall turned on. We made an exception for port 5555 (the default port used by our agent) and then the error stopped. You'll notice that the other post said this issue was fixed if they forced a sync from the server. That probably worked because forced syncs come on port 5556, which the firewall may not mind.
I had this happen at a previous company that i worked with. It ended up that our Trend Anti Virus program didnt play well with SafeBoot.
What we did was disable the Trend services and then install SafeBoot, after the initial sync was finished, we re-enabled Trend and everything worked fine.
It has also been noted that some newer AV/HIDS engines will detect SafeBoot DE client as a "RootKit". You may need to flag the software as safe.