What model battery are you using? The PC100 is a nice little camera, but it has a (nice) little battery. And due to the nature of the battery slot there are not a lot of options for a longer life battery. The battery that comes with the camera is the NP-FA50 (800mAh) They also sell the NP-FA70 (1220 mAh) Obviously, you should be using the FA70 if you want the longest run time. FYI, Sony's other battery styles go as high as 6600mAh so you can see that the battery for the PC1000 is limited and will need to be changed more often. You should get a couple of them.
Have you tested the battery life outside of the housing. Before you blame the housing, do some "virtual dives" on land and see how long the battery lasts. Walk around your neighborhood with the camera and shoot for an hour. Use the LCD and zoom in on things. Try and record as much footage as you would on a dive. See how long it lasts. I bet you'll find it is the same as in the housing.
I doubt there is anything wrong with your housing that would cause the battery to drain. Like Scubadru said, the lanc control does not draw much power, if any. The Mako's monitor back does draw power from the camera and that will certainly affect the run time. Just like when you use the flip out screen on land. If you only use the viewfinder then the battery will last longer than if you use the LCD. Same thing in the water. Using the monitor back will consume more power than the standard back. That's just part of the deal. The PC1000 is a great little 3 chip camcorder, but it has a puny battery.
So what's the work around? Make sure you have the biggest battery you can, and swap it out after every dive. If you can't get a full dive on one battery then you'll have to be conservative with it in the water. Turn it off when you are not shooting. The start up time is not bad when you are ready to shoot again. I know this sounds like a hassle, but the alternative is a larger camera with a larger battery (with a larger housing).
I don't think the Gates housing would be much different. The PCII is designed for the LCD screen to be open so it will have about the same power draw as the Mako with the monitor back. No real advantage there. You could use the Mako with the standard back, but I wouldn't. I like the screen too much to give it up for a few more minutes of shooting.
Good luck with your testing and I hope you find a happy result. BTW, other than the power issue, how do you like you Mako housing?
Danb