OK! Thanks for sharing a simple project to reproduce the problem, that makes debugging so much easier. This is a bug that is caused by the render setting "mix and process FX at project sample rate", when using certain render resample modes. We'll fix for the next release (which will be soon). In the meantime, as a workaround, everything should align properly if you either disable that render setting, or use the r8brain resample mode (which is the preferred resampling mode, anyway).
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