Hello Jack,
I had a similar problem with the FXTH87xx... Please make sure that you select a binary and a target for the project:
Select Bnary
1) Debug Menu -->Debug Configuration
-->Select the project from the left column.
2) C/C++ application ---> Search Project...
---> Program Selection Window (Select a binary to run)
--->Click OK

Select Target
1) Target Settings --> Edit...
2)Target ---> Edit...
3) Target Type---> Edit..
---> Select MPXY8500 from hcs08.MPXY

Hope it helps!
Josh