My weapons stop charging whenever an enemy ship cloaks. As in the bar is halfway up and stops filling.

Is this a bug or is there some way to force the bar to fill?

That is not a bug. Your weapons stop as long as the enemy stays in cloak. However if you cloak, the enemy weapons also stop.

I don't believe I've ever had this problem. Maybe it's caused by the enemy ship cloaking? However, I would think the weapons charge and simply don't fire, whenever the enemy cloaks.

---edit---
Never mind what I've posted. I was not aware of certain things.

Yeah, that being said, it's still best to wait until they fire and make them miss a shot before you cloak.

Basically, hit the pause button as they fire and cloak.

If you invested anything at all in your drive, the likelihood that they'll miss while you're cloaked will be very near 100%.

Mine is at 98% currently.