Hello münsterorganist,
[Topic moved here.]
You settings (such as voicing, and/or audio engine options, and/or or rank memory options, and/or audio routing, and/or convolution reverb settings) can certainly affect how any given sample set will sound. Hence if you have different settings between the two PCs then they could potentially sound different. You could use Hauptwerk's backup/restore mechanism to copy your settings from one PC to the other -- see the 'Backing up and restoring your settings and data: Moving your settings to a new/different computer ...' section in the Hauptwerk user guide for how to do that (starting on page 32 in the current v6.0.2 version).
Also, if the CPU cores of either of were PCs are overloaded, it could affect the resolution at which Hauptwerk's background models (especially the wind supply model) will be processed, which could affect the sound of pipes (e.g. brightness and tuning) to some extent.