Handles are more or less exclusive to the application using them, so in general, if ZA AV has an invalid handle, it would be it's own fault.
Now I have to agree that Spybot-S&D can kill handles even inside other processes - in extreme situations, it does that to kill handles to malware inside other applications to be able to delete them. This could happen only if you scan with Spybot-S&D and fix malware (exe/dll/sys files, not simple cookies etc.).
So if Spybot could be at fault, that error should not appear if you scan with ZA AV before Spybot after a rescan. Thinking that you probably are not permantly infected with such files (in which case you wourd be asxing different questions first I guess

), I regard this as unlikely though.
In general, "Invalid handle" is an error messagetype reported by the system to an application, but absolutely no error message that should just be passed to the user, since A. it does not tell the user anything useful, and B. until its accompanied by additional. information, it does not tell the developer anything useful as well

See this
blog entry (hmm... probably not online before Monday... I wrote a draft on how software developers should design error messages, since I regarded this as useful as a guide for our Spybot 2.0 handling).
Back to topic... Spybot can scan the bootsector, again only when scanning. It then looks at it in a nonexclusive way only though, and I'm not even sure that is already used in our detections, since boot sector things are usually AV and not AS things. Again, if Spybot would be part of it, ZA AV should rin without this error if you run the AV scan before any Spybot scan after a reboot. Not that I believe looking at the BS on our side could cause any conflicts there, because it really is very simple.
Do you have the full, exact error messages? Maybe they would tell us more.
(and this is btw why I recently
wrote that we currently could not recommend any firewall... they're all trying to be in do-it-all solutions, spreading from the point where they are good at).