Thanks for replying! Yeah, I know it's pretty old at this point but I think I grabbed it in a humble bundle some years back... It kinda just sat there in my steam library ever since, though the newer versions definitely look tempting.
Anyway, here's what I mean - the transparency on the B tileset is fine, but the "border" of the wall is from the A tileset, and as you can see it has that blue/black grid still showing? 
Viewing post in Modern interiors - RPG Tileset [16X16] comments
Ohh I got you now! Unfortunately you can't use that tiles to create an inner corner if the software doesn't intend them on different layers! Now we have 2 ways to fix it, tell me which one do you prefer:
1) I split the A5 file into 2 files so I can add more walls and ceilings options that exactly fit the tile size
2) I add the walls and corners options to a generic B-C-D-E file, so the software will intend them on a different layer