Jim,
I don't have this problem, but I have a vague recollection that I have heard it at some point in time. Just to help me get a little more insight into your set up, could you please answer the following questions.
1. What are your settings for the Count-In / Metronome?
These are found via "Prefs" (#1). Count-in/Met (#2) on the below image. The image shows my settings. Is there anything in your setup that is different from mine?

2. Do you have looping engaged?
On the image below, you can see that I have "NEVER loop entire song" selected.

3. Do you use multiple choruses?
As you can see below, on my setup, I only select a single chorus.

If you can answer the above, it will help me try and isolate what might be causing it if Mac's suggestion of returning to factory settings doesn't bring relief.
Regards,
Noel