Hello Don,
Could it be that your PC's CPU is being too heavily loaded? Does Windows Task Manager show very heavy CPU loading at the times that the tremulants slow down excessively?
Hauptwerk gives priority to the audio engine over the tremulants in times of extreme CPU load, to try to avoid audio glitches (since an audio glitch would probably be more catastrophic in a live situation), but extreme CPU loads can certainly cause the tremulant model and other background models to be 'choked'.
If that doesn't solve it, can you send us your CODM organ definition, the 'full-format' organ definition generated from it, and also a diagnostic file ('File | Create a diagnostic file'), so that we can see if we can reproduce it here with your organ definition and settings. Thanks.