While that's good advice, we've done that already. When we updated from 1.07 to 1.08 we had no mods at all. Had mods installed on 1.07, but prior to the update to 1.08 all mods were removed so the update process wouldn't be interfered with by any mods.
The problem existed immediately after update, prior to reinstalling the mods we use.
Many of the files we had been using before the update were then copied back to the server after update, such as our types.xml file (1.08 installed a default types.xml and ours is edited, so we simply copied and pasted the one we use back overtop of the default on that 1.08 put in place) so the possibility exists that one of the files we use for the older version is somehow preventing the actual placement of items. However, this shouldn't be the case as none of those files, to my knowledge, affects how things are placed. It's once again a case of "if i knew which file handled the ability to place objects I could check, but I don't know that file, because BI hasn't given anyone any instruction manual at all on how all this stuff works or at least which file does what".
I have not heard of any problems with re-using 1.07's XML files but if there is a problem with that that anyone knows of I'd love to hear it. I don't know if they changed any class names for any items, no announcement has been made either way on the matter, and I'd like to know for sure whether all class names are the same or if they changed them.
Anyways, long story short, the tl'dr version of this is that the problem has existed without any mods because we've done that already. Good advice, just, we've already done that,