ID:2446632
 
(See the best response by Nadrew.)
Problem description:
In Options/Set Map Size I set certain map Z locations, yet they aren't that Z value in game. What am I doing wrong to not have the Z locations properly set?
When you have multiple map files included, they stack in compilation order.
I named them accordingly so that their compilation order is the same as their Z location order. There's maps from 1-13, as well as 16-17. However, There are several gaps between the maps in Z location that don't match up with the specified values. Like the map with the specified Z location of 8, due to all the random Void gaps, in game its Z location is 29. I tried clean compiling and deleting the backup maps folder, but nothing changed.
Best response
Say you have these maps included:

1.dmm
2.dmm
3.dmm

And those maps all have a single z-level you'll have them where you expect.

But if for instance, 1.dmm has 3 z-levels, the stuff in 2.dmm will begin at z-level 4, and so on.
How do I check if a map file has multiple Z levels?
Open it and see if the little arrows that switch between levels are enabled, or use 'set map size' from the menu and see if the z value is more than 1.
Alright it's fixed, I thought the Z value in Set Map Size was to designate its Z location lol. Sorry about that, and thank you for the help.