I think that this may be a problem, specifically, with fleets, although I'm not sure. I'm having an issue where ships (a fleet) will not move when I select a destination that is more than four or five parsecs away. I know it's not a range issue, so it's pretty strange (for me). I can move them a few squares at a time, but never longer distances. The destination marker simply doesn't move. When I click a space, the ships will actually show in their statuses that they're going there, but they change their mind immediately after.
I noticed this occurring on the first mission of the Dread Lords campaign. I'm playing Dark Avatar, version 1.80q100.