Looking for computer upgrade help for our MAT 252 Kiel III instruments

We have Isodat 2.0 (SP 2.67) running on an old Gateway (450 Mhz, 128 Meg 
RAM, Windows NT 4.0 SP5).  No problems.  However...

We are trying to upgrade to a Dell Optiplex 780 (Core2 Vpro, 3.16 Ghz, 2 Gig 
RAM) and appear to be having communication(?) problems.  The sequence will 
start running but as soon as both the Kiel (carbonate isl?) and MAT 252 (dual 
inlet isl?) start to run together we observe odd readings on the screen.  

For example... with Trap 1 at 150°C (pumping out) and Trap 2 at 30°C (full of 
CO2, ready to analyze), the T2 reading will flicker between 150°C, 30°C, 19°C, 
38°C.... When Trap 1 changes to -190°C (during reaction 1 on the next 
sample), Trap 2 will flicker between -190°C, 30°C, 19°C....  

In addition, the data on standards are simply nonsense.

Has anyone had this type of experience in attempting a computer upgrade?  
Any ideas?