So don't even begin thinking along those lines. Those files in the SBS Store folder are purely historical in value and are already processed, so removing and/or leaving them makes no difference at all.
The problem is a timing issue most likely. Most likely, the system being rebooted is getting there before the SBS file is received by the SBS server. We used to call this a "race to reboot" condition. We don't see it anywhere near as often as we did in the past.
I would actually recommend you call this in so we can troubleshoot it and possibly log something against this.
We are, by the way, working on a permenant fix for this by modifying the way the PXE server is updated. One suggestion, for instance, is to make a request in real-time for what is needed with a client rather than relying on a file-transfer methodology that might get delayed for any number of reasons. We know this CAN happen, and that's why we're looking at alternatives.
Still, if it's moderately reproducable what you're seeing, we should capture this.