Aamorin,
We did find a way to control the 2 position valve, but it was extremely difficult to get direction from Varian and impossible from Valco, but in the end one of the Varian technical people did have an idea.
What we wound up doing was using the relays from the CP4900 and wiring it to the two position actuator. Here is the link for the VICI relay device on pages 3 and 4, we used mode 1.
http://www.vici.com/support/tn/tn413.pdf
To connect to the CP 4900 you need to use the Digital I/O 25 pin port and I believe you need to connect to pins 13-16. (please double check this in the Varian manual, its the general manual that comes on the CD; should be around page 48) If i remember correctly 13 and 15 are common and 14 and 16 represent position 1 and 2 respectively.
When configuring this in the Galaxie Configuration Manager remove the Valco driver and do not use the VICI valve automation. Instead use Relays 1+2. I don't believe you can test this till you run a method, so you may need to create a new method with the Relays attached. When you run your method their will be an option that says Vial, put 1 or 2 in it to correspond to the correct position (A or B). Also we were told that we needed to put in a value for Injection volume (this is actually a time volume in minutes so i suggest making it short ~ 0.05 min). But for some reason we were able to run with no problem by keeping that value 0.
This should work pretty well, we were able to get consistant readings after connecting this.
Let me know how it goes.