You might have troubled yourself to mention the vendor of the instrument. For connectivity issues, Agilient's aren't Waters aren't Shimadu's aren't other vendors, as an example. For results with the same sample, sure, all instruments are somewhat equivalent, but this is hardware.
[ETA] Ah, I see the link now.
Generally, the vendor provides a functional PC. and connects it, for industry or university setup. But maybe, for some reason, you're on your own. But I'd call the vendor.
I don't see why you assume you can use the 64-bit version of Windows, if the software isn't written for that. That will always fail.