Try to "reset" the ACC (press [AUTO] and [<=>] simultaniously). The LED's
start to light up one by one, and the temp indicator shows "0". The whole
proccess takes about 30 seconds. If a fault is detected, the temp display
will show the error number (i don't know these numbers, sorry). If
everything is OK, the ACC returns operational with the default settings. It
worked fine for me...

Good luck!

I've experienced a like problem w/my '88 9Kt - the CSE has a newer
system, yet in principal they're likely have the same design function,
i.e., the 9k's ACC is designed so that in auto, the ac compressor  is
always on, and the difference between heat and cold air delivered  is
based upon the opening/closing of a door to allow in heat.  When the
servo motor goes, the flap of course no longer moves automatically.
There is a diagnostic procedure, but on the CSE, I've not a clue as to
what it is.  From memory, the code for the above situation in the
early 9k's was "5C" which the factory service manual identified -
again by memory - as 'reversed polarity.'  

The servo in question resides just to the right of the ashtray/radio
cluster.  You can see it from there, but side with the control rod
faces the right, ergo you will be unable to see how it is fastened.

I had similar heat conditions with my 1992 9000CD, it was the plastic
level arm behind the firewall that broke, this controls the opening and
closing of the heater core.  Saab has a kit for it and replaced the arm.
Suggest to reprogram first and then check the heater arm if still not
working.

Oscar