Sometimes when morphing into dragon form all untis turn invisible and remain so, including my own, no matter how much i zoom in. I can still attack and order them around since the unit Icons are still visible, It's as if the texture just disappeared.

Does anyone else get this? right now I got all the options cranked up to ultra, though i'd gladly set them lower to be able to actually see them

I have not seen this reported before. It couldn't hurt to try a lower texture quality.

Are you forcing AA in your video driver settings? That can cause graphical problems.

Try contacting Larian support (see below)

Dragon Commander - troubleshooting and support