I've tried rearranging the stacking order of the consolidated haks in every possible combination (there are seven in all, as opposed to the original 30 separate ones), but to no avail.
The module is planned as multiplayer. I fired it up on the NWserver, and then logged in on a separate computer... and the missing doors are all there. It's only on my regular computer, where I'm designing it, that they never show up now.