Hello Max,
[Topic moved here.]
You need to set the host project's sample rate set to the same sample rate that the organ loaded in Hauptwerk uses/requires (48 kHz for most commercial sample sets, but 44.1 kHz for St. Anne's). Here's the relevant excerpt from the 'Using an AU/VST host to apply real-time reverb' section of the main Hauptwerk user guide (page 184 in the current version):
"Create a project in your AU/VST host software for the organ (sample set) you intend to use, and ensure that its sample rate is set to the sample set’s native sample rate (otherwise the organ may sound at the wrong pitch). If you use several different organs then you may wish to create a separate project for each distinct native sample rate they use (such as 48 kHz and 44.1 kHz) and load the appropriate one with each organ according to its native sample rate."