EDIT: I re-read kaboom's post. I thougt I understood, but I didn't. I originally thought he was suggesting to make a new map and completely copy all the terrain I already have into that new map, but I think he means to go into xtra and use its terrain editor to get rid of the square terrain.
Even in xtra editor, when I try to make terrain, it is in rectangles, and not normal. It is like the oldskool days of square terrain where you used ISOM; you just edit the map so the normal editors create rectangular (2x1) terrain blocks.
/EDIT.
Kaboom, I actually understood your post, contrary to corbo's. Two things, however:
1. I placed this here instead of in the terrain section because the terrain section has to do with the terrain that people create. The question I have is concerning my overall map status in which I cannot create normal terrain. Besides, the terrain section is all people showing their custom terrains with the pallette, not isometric terrain.
2. The idea of making brushes is a great idea, kaboom, but unfortunately I cannot execute. There are many triggers on this map, and it would probably be faster to do the rest of the map just copying different sections of my map I have already made than to re-do all my triggers. However, this would still be a complete and utter pain to do for an entire 64x128 area...
I pretty much need to know how to either
a. revert my map somehow using a program like ISOM that allows it to no longer automatically create rectangular terrain.
or
b. find a program that can do isometric terrain even when the map default is for making rectangles. The problem with this is is that SCMdraft can do it, but it crashes whenever I try to place terrain on the map.
Thanks for the help so far... I appreciate it, and I hope someone can come up with a better answer than my idea of making isometric terrain manually with squares and the palette

ADDITION:
I have come up with a solution to this problem; using scmdraft, I copied all the terrain over to a new map of the same dimensions. I will edit all of the terrain on this map, and once I am done, I will copy it back to the map with the triggers.
If anyone knows how to revert my original back to the state where I can place down normal terrain, I would still be thrilled to hear how; copy pasting terrain so large is a pain. Also, when I go to edit my already-placed terrain, it completely treats all the pasted terrain as if it isn't there. I am still open to suggestions, especially about on how to revert the map, but this is the solution in which I will execute if no one is able to come up with anything.