2008 Cobalt radiator fan stays on if battery is connected

I replaced the engine in a 2008 Cobalt LS(2.2l). While running the engine, I noticed that the cooling fans didn't come on. I found a bad ground for the fan motor and ran a new ground to the upper radiator support. After installing the new ground, I noticed that the fan stays on all the time. It is at a speed slightly lower than "low" - I can command the low speed fan on with a scan tool and the fan speeds up slightly. If I command the high speed fan on, it speeds up significantly. There is 12v coming out of the under hood fuse box for the fans at all time. I removed the fuses and relays for the fan and it still runs on this super-low speed. The wiring diagram I have shows a constant ground on the fan motor with relays switching power to the different windings in the motor.

I opened up the fuse box and noticed that the solder joints on the diodes for the fan relays were discolored like they got very hot. I checked resistance across the diodes and neither way read "OL" like the other diodes on the board did. I then cut the diodes and reassembled the box. The fans did not run unless I commanded them on with the scan tool, when I did, they worked normally. I ordered a used fuse box and installed it... same exact thing as before - fans always on. So I opened up the old box, soldered two through-hole diodes on the SMD board and reinstalled that box in the car. The fans went back to always running.

What could be going on here?

Thanks for any input!
-Jason