This actually happened to me when running on real harware. The person who I bought the 128 from replaced one of the CIA's with a 6526A, which is used in the 1581 and Amiga.
While it is pin compatible, and everything "looked" okay. The Machine booted. My clock would stray WILDLY!
Check Settings > Machine > Model.
Make sure you have the following set
Model (Any NTSC model)
6567 (NTSC)
Power Freq (60HZ). - As this might affect TIMING.
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