Auto-Align looks for correlation in the signal and will set the best settings to achieve the best phase correlation. It is possible that playing different sections of the tracks or if there's a bleed from other mics, Auto-Align will decide on a different settings.

In such cases, we recommend to use the Noise-Floor faders on the Receiving channel to filter as much bleed as possible from entering into Auto-Align's detection analysis. Setting the Noise-Floor to just a few dB's below peak level, will allow Auto-Align to concentrate on the transients of the drums and will generally produce more consistent results with a complex signal. 

On the other hand, If the drum track is built using several different takes and the mics were moved between takes, that could also explain the effect.