Dear, I was for many years FSE of PerkinElmer, then I was ASP of Agilent.
I set up a service laboratory and bought 02 Varian GC-MS systems for use in my laboratory, I had communication problems just like you and I managed after many attempts to solve them.
I will try to be of some help in solving the connection problems CPU - GC - MS
We have 02 GC-MS Varian systems in the laboratory - Saturn
01 - GC 3800 with 02 FID detectors and 01 Saturn 2000 MS / MS
01 - GC 3900 with 01 Saturn 2100T Detector with 03 keys for MS / MS.
I faced many problems to be able to configure these instruments each time I upgraded Windows (95; 98, 2000; XP SP2; XP SP3), and the Saturn Workstation software (Versions 5.1; 5.4; 6.2; 6.42; 6.9 and 7.1)
I tried many CPU configurations with PCI-GPIB cards (Varian, Isatech, HP-IB, National Instruments), I bought SAP Waveboard control cards (Saturn control and communication board) without solution
When I was able to get the 3900 - 2100T to work with a set of hardware / software, the same configuration did not work on the 3800 - 2000 MS / MS.
Both systems were supplied with Dell Optiplex CPU with a PCI-GPIB National card and worked perfectly until Windows 2000 / Saturn V.5
These systems worked perfectly with Windows 2000.
When I upgraded Windows (2000 => XP) and the Saturn WorkStation Software from version (5 => 6.2) the 3800 - Saturn MS-2000 system stopped communicating with Saturn. I updated all the National card drivers, it still didn't work. I downgraded Windows (XP => 2000), and the system went back to working perfectly.
Not satisfied I upgraded to XP + Saturn Workstation 6.2; then 6.42, 6.9 and 7.1. No software communicated with the MS.
Then I installed Windows 7 with a virtual machine 2000 / Saturn Version 6.42, success!
However, I was not satisfied, some time later, we had an electrical problem caused by the power utility and the two CPUs had their source damaged.
I then bought two non-branded CPUs and installed both systems and surprise, both systems worked perfectly using XP-SP3 + Saturn WorkStation 6.9.
Finally the two CPUs we bought from DELL Optiplex arrived, so I migrated the systems to the new CPUs. Frustration, the GC-3800 / MS2000 system stopped working. When you put the CPU xingling the system worked, when you put the CPU DELL the system did not work.
Not satisfied with using a CPU with no defined brand, I decided to investigate the problem in depth and using a National program tool, supplied with the GPIB card driver, I found that the communication did not start, I verified that the DELL system + PCI-GPIB + network card 10-base-T ethernet is incompatible.
Then I bought a media converter from Black Blox 10-base-T ⇔ RJ45 and then it started working sporadically, sometimes it communicated, which forced us to never turn off the system to avoid headaches.
I bought new PCI-GPIB cards and it didn't solve anything.
I switched back to the non-branded CPU’s and everything worked perfectly, so by isolating the variables I verified that the DELL CPUs are incompatible with some Varian Saturn instrument configurations. However I was not satisfied, I wanted at all costs to put the system to work using the CPU’s DELL.
As we have an Atomic Absorption SpectrAA 240 that uses a USB-GPIB-HS card from National, I decided to use it to test on GC / MS and voilá !. All two systems working perfectly using Windows 7 + Saturn Workstation 7.1.
Lauro