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So, here's quite a doozy for those interested.

Program A outputs the contained "Map" file in Array format, where Blacks are 3s (Walls), Dark Grays are 2s (Floor), and everything else is 0 (Empty). It can both save and load .flr files with no problem, and the map returns the same each time. Program B, shown, reads both 2 and 3 as if they are "Walls" creating huge blocks of unexplorable space. :\ Obviously there are much larger dents in the program currently, it's very far from the "Huge Dungeon Tutorial" that I took some of my inspiration from, but at the moment I have no clue how this wall thing could possibly go wrong. For those interested, you're free to use the rest of the working program as an example, but this is far too simple for anyone remotely capable of helping me with my actual problem.