The pilot gets cloned every time he goes back inside the craft, and leaves a body on the ladder, which then has to be removed before the pilot can exit once again, to get cloned again on entering. The pilot clones left outside cannot be erased through flight tracking. The install was clean, but I'll try it again. I did the Mega one through Chrome which didn't require an add on.
I have an issue where when I reenter a capsule with a kerbal, the kerbal body will be left outside, as a blockage. On the ground, I can spin my capsule to knock the kerbal off the ladder, and then create dozens of kerbals in this manner. However, the flight center cannot erase these kerbal clones. Any fix? I might try erasing the mod which changes the models for my brave little kerbals. Also, I have all the newest stuff running.