When Fusion is calculating grid widths on regions, it loads the blocks in each region from core block placement and blocks placed with the context module.
The context module has a region reaction which disables a region by removing blocks from the page array. Since Fusion counts the blocks by directly accessing them from core and context the region disable reaction doesn't notify Fusion that it is disabled. A solution for this is to alter the fusion_core_block_list() function to also check the region reaction.
I have included a patch needs testing.