I just fought the Flagship for the first time, to a mutual kill (which of course counts as a loss).

During the fight, when they went into cloak, my weapons stopped charging.
This looks like a glitch. Has anyone else experienced this or contacted Subset about it?

Glitch or designed, I feel robbed of a win... :/

yup thats what cloaks do
they freeze your weapons ability to lock (hence charge) for the duration of the cloak

Enemy cloaking devices do stop your weapons charging - it works both ways as well, so if you get a cloaking device you stop enemies from charging weapons for a bit. You can't lock on to what you can't detect. :)

If it's any consolation, there's a bit more to the flagship than that. :)