I am a pretty regular sewing machine user but I don't know anything about even the most basic troubleshooting. I can't tell you why your bobbin thread isn't getting picked up.
But I do have some experience making seams with cuben and U-09lv. How are you applying the glue and securing the material during curing?
I think your sewing machine should have no problem sewing through the bonded cuben, and the bond may be strong enough to make sewing unnecessary, if the glue layer is thin enough. The bonded seam should be almost invisible and not perceptibly thicker or stiffer than the cuben itself. The way to do this is by clamping.
First, I refrigerate the glue. This increases it's viscosity a little (it's still more fluid than U-09fl), but, more importantly, it increases the open time. I apply masking tape (a blue kind for delicate surfaces) on the side to be bonded of each piece of cuben, about 1/2 inch from and parallel to the edge. I then apply the cold glue to one of the surfaces with a tiny plastic paddle, making the layer as thin as possible. Then I mate the two surfaces so the edge of each piece comes right up to (but does not overlap) the masking tape on the same side of the other piece of cuben. I then put a long strip of painter's plastic over and under the glued seam, and then a long strip of very thin foam (fleece or terry cloth would probably work, too). I have two, seven foot pieces of very smooth hardwood moulding. I put the glued seam, sandwiched between the plastic and the foam, between the wood pieces to cure and weigh the top piece down with several hundred pounds of weights. Large C-clamps could be used, too. This forces the excess glue out of the seam and onto the masking tape. Because the glue was cold, curing is delayed just long enough for the excess glue to flow out onto the tape even after ten minutes of fiddling with the foam and the weights.
After about an hour I disassemble everything (carefully) and very, very gingerly peel off the tape, and with it the excess glue. The glue is not cured yet, and the seam can be easily peeled apart at this stage, so be careful. If you wait longer, though, then the glue becomes stronger than the tape and getting the tape off becomes a disaster.
This is the best method I have found for achieving very strong, invisible cuben seams with hysol.
I hope this helps.