Ray A,
It sounds like your ISR is overwriting the values in the accumulator. I would check to see if your Program Status Word (PSW) is properly being pushed and pulled from the stack upon entry and exit from your ISR.
Here is the link to the RL78 software manual:
http://documentation.renesas.com/doc/products/mpumcu/doc/rl78/r01us0015ej0220_rl78.pdf
I hope this helps.
Mike Clements
RenesasRulz Moderator