When you wrote "pumps" I assume you meant "channels." First, is your degasser working? bubbles could be forming in at the proportioning valve which would cause low, irregular flow. Your gradient proportioning valve could be bad. Try moving the water to a different channel and try the flow rate at 50:50 again.
There is a routine test for proportioning valves where you put 0.1% acetone in B & D, and put clean water in A & C. Monitor UV at 270nm. Then run a stair-step program at 0, 1, 5, 50, 95, 99, 100 and compare the levels of the steps to a theoretical gradient; do A-B and C-D.
Your buffer might be precipitating in the proportioning valve and the crystals get stuck in the check valve. If your mobile phase is right on the edge of maximum solubility, this can happen.