the aux water pump does not run always, it starts only when heater is on and the coolant is above 30 degree Celsius and when heat is needed depending on the settings on the thumbwheels on the control panel.
It pumps 950 l/h. Here is a 53 pages tech info in German language how the system works
http://www.e38.org/e32/klimaautomatik.pdf
even if you do not understand, you can read the drawings, aux water pump control is in section 5.8
Maybe the control panel/module is defective.
IHKA pinout
http://www.bimmerboard.com/forums/posts/426626/
heater valve pinout
http://www.bimmerboard.com/forums/posts/841827/
wiring diagrams
E34 (1988 to 1995 5 Series) Wiring Diagrams