I seem to be having a similar problem.
I downloaded a region from the exchange, uploaded it originally and it worked, rendered and everything. The problem was, it was an enormous map, like 64X64. I wanted a smaller map so I opened up MS Paint, reduced the size of the config to 24X24, saved it as a .bmp, took the already grey-scaled map and reduced the dimensions to 1537X1537, then saved it as a .Jpeg. When I load the game the config map comes up right away but when I do Shift+Ctrl+Alt+R and find the greyscale map and double click, nothing happens. Everything is in the correct folder and everything.
I literally have no idea where to go from here. Please help!