Hello,
Indeed, I'm not surprised it doesn't work better after have upgrading the firmware 3.03 is the same than the 3.02. Brücker has acquired the 4x0 GC series and then this firmware is juste the "Brücker designed".
I'm surprised that Brücker just told you to upgrade and didn't help you more...
If you have a message in Galaxie saying that there is a setup or config issue, it means that there is a setup or config issue between the GC and the method. Certainly the GC config has changed (even a little thing), whereas the method has been created using a different configuration.
If you trust the GC config, then, I'm afraid you will have to recreate the method from scratch.
You should contact the Galaxie support at Brücker, they should be able to help you.
Which firmware were you using before changing the faulty board ? Also, after have changed the firmware you should upgrade the Galaxie driver, as the communication "module" depends on the firmware used. So if you use an old driver version, it may not work with a recent firmware. Do you know which driver version you are currently using ? You should use the driver version from 1.3.2.436 (cf the VARIAN_GC450_IMM.dll file version located in the C:\Galaxie\Server\Devices folder)