I faced a rather strange problem with my map. After editing the map in ZE for a few height and terrain changes, I munged it normally and during the testing, the map that was played out was the old one before the changes. I also turned on Uber mode on and off for testing before, so could have have anything to do with it?
Other maps made before never had that problem. I tried a manual clean and looked at Teancum's tutorial on manual cleaning. However, I did not have a "SIDE" folder as stated in the tutorial. Is is another variation, or is something horrendously wrong.

Thanks, possible solutions much appreciated!

If you have no custom sides, you shouldn't need to manual-clean any sides folder.

Could you post your error log?

just thought i would state the obvious, but did you save? open your map back up in ZE and see if the changes appear there. also make sure that you didnt accidentally uncheck the [common] box when munging. And were you in the base layer when you made the changes in ZE?

The only things that were changed was some terrain height (cover some roughly shaped objects). All of it was done in the Conquest layer. I saved and load like around 10 times, so I am positive that I saved correctly. Is it possible at any rate that a residue file may be negating these changes?
And there were no errors logged, so its probably that the wrong stuff is being munged.

The common folder has basically no effect (It contains common objects, scripts, and the like.) on the world as seen in ZE, since it doesn't contain any info on terrain height, object placement, etc.

I know this isn't a bright question, but I have to be sure: You have actually munged after the manual clean, right? As for the residual file question, that's percisely what a manual clean eradicates by not only erasing the munge data used internally by VM, but also by deleting the files copied over into the addon directory on both ends, so they are all freshly compiled when you remunge.

Ubermode, being a bit of text contained in your lua script, cannot affect your world's ability to munge.

Any chance that the files are corrupted? I am saying this because in the wrong (old version) of the map, some floating CPs were found. (Not supposed to happen in old version), most likely a height error which is starting to become more serious(for my other maps).

Come to think of it, make a change you know for sure you can't possibly miss (obviously, save and munge), and see if it shows ingame. You don't have to keep the change, since it's just a test. That will tell you for sure if the changes are being munged or not since you've cleaned.

It's actually very rare for files to simply become corrupted, since you'd have to have a really messed up computer in order for that to happen with any regularity. Most of the time, the source of such headaches is the human factor.

As for your floating CPs, ZE is not always a precise representation of your map ingame, though it usually is. I've often noted ZE changing values on it's own in animation mode, objects that show up ingame slightly off from where I placed them in ZE, and even objects whose orientation in ZE is not the same as it is ingame. The only thing you can really do is reposition things how you want them, unless you want to change the object's coordinates directly, in the lyr file.

Have you changed the size of your terrain at all?

Size stays at default of 1024.