The reason I need to do it this way is that the site mesh comes with the surveyor datum as a reference point, wheres the geometry comes from Maya in multiple bits and pieces, so I'm trying to avoid repositioning geometry to the correct hights but rather have the import done into AC's absolute zero.
Which means my geometry will be at zero and my site will be placed under it (or in this case 1677' below it)
the point is; that everyone I've asked seem to face the same problem with creating stories in an elevation below -328' which might be a bug (since there is no problem placing objects anywhere below that.
Meanwhile I found a way around it.
It seems that if I change the "hight to next" field to the number I need, while setting the floor above hight to zero, AC brings it to correct elevation hight (even though each time I highlight the story the elevation level goes back to -328"