Yes this is what I mantioned to Wulf in another post. I been unloading zone manager, building, then re loading zonemanager. Also building outside a zone isn't a problem.
So in general, players don't build inside a zone anyway, but you need to make sure your building blocked area extends beyond the zone so people cant build after you load zone manager.
Obviously zone manager is awesome even if this issue persists.
So just get your admin structures up like arenas, shops, rifle ranges, then load zone manager.
edit:
It isn't zone manager only. I just unloaded it and the server just crashed again the same way.
This is driving me crazy because I just built roughly 7x7 9 floor with bgrade working now w/o zone manager and no problems.
Even with zone manager for a while. Now zonemanager is unloaded and it just crashed again.
Also pasting a base in the zone is no problem FYI.
The other opotion is do server.save every time you get a little done. At least when it crashes, you won't lose up to 5 minutes at a time.