Since updating to 0.9.4, I am finding that the military intelligence green/red grid squares on the map are no longer updating - I downgraded to 0.9.0 with the same map and this feature functions without issue.

Were there any changes made in the new version regarding this feature that I need to accommodate?

Just to clarify, this is actually impacting all of the mil int functions - I am not seeing friendly unit markers anymore either.

Agreed, no squares are highlighting for me or my clan either.

Yeah same here. Despite Player Command module settings, the sector coloration is gone as of this latest update.