I understand that scheduled launches can turn red in the time machine, and the clock blink red, because changing game mechanics make that future launch no longer possible. But I've been seeing it happen at other times - when the launch is still perfectly valid. Anybody know what this means? I can't figure it out.

As your knowledge of the world around changes the predictions of the time machine change - sometimes making future moves non valid.

A specific example is when you are near your driller cap

You want to send 20 drillers from factory X as soon as they are built - so you pre-order it. Sometime after the order is set you gain control of another factory and so you therefore hit your driller cap before 20 are made at that original OP - making the order turn red.