Luke, burning the midnight oil, eh? This must be bothering you to keep you up so late - I know the feeling .
From your description of the 'symptoms', I'd say the first place to look is the skimmers (as the bubble lessens when they're closed and gets worse when it's the only line pulling). I assume that the two skimmers are tied together. Do you have pressure testing apparatus? , I'd pressure test the skimmers - if it's an above ground leak, you should be able to see water 'weeping' out where the line is bad, and the test will tell you if the line is compromised. As another question, is the plumbing 'black poly'?
Actually, the first thing to check is if you can see bubbles comming into the pump? The first thing to do is make sure that the lid gasket is well lubed and in properly and that the drain plugs aren't pulling air (as Al said, a small leak won't drip but under a vacuum will draw air). If you see air comming into the pump with the MD off, you can direct a dribble of water over any suspect connections (the pump lid, any glued connections, the plugs, the VALVE, any threaded connections), if the bubbles start to disappear - you've found A leak! (though sometimes there's more than 1)
Please keep us informed as to your progress and/ or any further questions on this - Good Luck with it!