It sounds like a race condition; you want the CrowdStrike updater to start and pull down the fix before the affected virus definition file is loaded and kills the box.
If you keep rebooting, you eventually may get those to load in the right order.
Anyway, had that confirmed by whoever is in charge of security and whatnot, as we have an internal StackOverflow clone and someone asking the same question was pointed to a PowerPoint presentation of dos and don'ts.
If you keep rebooting, you eventually may get those to load in the right order.