Hi Alice,
I apologize for the delay in updating, but I've finally gotten to the point where circle back to this issue.
I've found that if the P&E OpenSDA program is being used to debug the target, the target does not start when you connect the USB. If I use the USBDM OpenSDA program instead I do not have this issue, and when I connect the FRDM board via USB the target begins running without having a debugger launch it.
Since I'm moving to the USBDM as my debugging tool so that I can debug and program a slightly different KE06Z chip, I don't anticipate looking into whether the P&E OpenSDA can be configured to let the target run on power up.
Interestingly enough, I've found that USBDM causes the target to run at an incorrect clock rate. I've started a discussion of that issue here:
KE06Z Clock Rate when using USBDM
Stefan