In some scenarios Auto-Align would init parameters incorrectly under SONAR.
If you notice the plug-in initialized incorrectly (for example it shows -10000 samples that means it'll play -10000 AHEAD of time). you should load up the attached .vstpreset as a workaround. (under the VST3 menu on your plug-in window)
This is only relevant to Auto-Align 1.5.3 and below and should be resolved with newer versions.