Lesley,
I wonder if this strange behaviour arises from one or more tracks being frozen. (I thought that tempo stood outside of freezing but I might be wrong. It's also possible that absolute tempo stands outside of freezing but percentage tempo does not.)
To test these possibilitie....
1. Make bar setting changes using %.
2. Unfreeze any frozen tracks.
3. Regenerate song.
Now repeat the above except instead of using %, use absolute values.
Was the behaviour the same?
Regards,
Noel