I don't see any obvious installation issues that make me say "AH-HA!"
Worry about one thing at a time, and go from there. First, you are concerned that your flows are low. I see that you have an extra zone on your manifold. Either tie that together or use an old washing machine hose between the drains on your supply and return manifold, then use the drain valve to throttle flow between them while you monitor amp draw at your radiant circulating pump. This will tell you if you are flowing, and you can monitor flow at the same time. If the amperage is quite low and then increases when you bypass the radiant tubes, then I think it's a reasonable bet that you're air bound. If it doesn't, and your pump is at FLA, your flow meter is lying, and you've got the flow you're going to get. If it doesn't, and your pump is not at FLA, you've got more system head than you thought. Either let it run in that condition, or open your bypass a little and get the pump up on its curve, which will have the added benefit of decreasing your delta T.
Second, I also think that your head and flow calculations may be off a little, but I don't think it matters. You've got a cold slab on grade, insulated but not overly, and it's taking a lot of water to get that heated up. You're controlling the slab by the space temperature, which has its own set of consequences, not the least of which is that at low space loads the system isn't going to run long enough to warm the slab, which is going to keep the slab cold enough that your deltas are going to be high because the slab is sucking every BTU out that it can.
Third, I don't think the delta T matters nearly as much as you do. It's a matter of heat, not of temperature. Your return water is approaching your slab temperature because it's not running long enough to warm your slab. If you drop your supply temperature, your pump will run longer, your slab will warm, and your deltas will drop. Not as far as you think, but a little bit of cold return water in as much volume as that boiler holds isn't going to hurt anything, and will actually help.
Take home: drop the supply temperature to design and let the system run. Keep track of pump run time with a plug in timing device of some kind if you like. It's going to increase at lower temperatures to keep up with load, but unless it goes to 100% and the room cools off it won't hurt a thing.
