This is happening every time I play a game, tested over a several day period. I queue orders on my capship, and sometimes (not all the time), the queued orders go unfulfilled.
Example: Click on vasari space whale, tell it "kill this siege frig, colonize the planet. then jump out to this other planet." Will look back later and see the space whale just sitting there. It killed the unit but didn't do anything else. In my current game (it's running paused in the background so I could make this bug report) I clicked on the desolator, told it "kill this unit, then jump to this planet." It just killed the unit and forgot the other orders.
I have verified that the orders are received properly, because I hold down shift and see the orders (kill this, colonize that, jump there, etc). They just go unfulfilled.
It could be that this is happening with non-capships as well. I'll lose units (migrators and such) by telling them to execute a series of moves. My suspicion is that they just do 1 or 2 orders, then stop and sit, meanwhile a neutral or enemy kills it. However, I have not formally verified that this is the case. But it's definately the case with capships.
Has anyone else seen this behavior?