Hey Beat,
Thanks for your attention in this matter.
As far as I can tell, Yen does not convert to decimals like other currencies-- it's all integers. This is what was causing the PayPal error. I changed the CB Subs settings to never format to the two decimals and this went away.
However, none of the subscriptions were ever represented as decimals. This makes me think that potentially CB Subs did a conversion to dollars, subtracted the difference in plans (to pro-rate), and then converted back to Yen. So this may still be a bug, albeit one that is easily worked around- I don't know. <shrug />