Undocking/Staging causes the vessel not being used to change orbit

[raver20999]

I have noticed that when I undock or stage the craft that is not continuing on orbit gains altitude but loses its orbit. Example: I've been trying to create a combined space craft with a altitude of 250 km above Kerbin. When I add a new section to the spacecraft I usually have the section attached to the upper stage with its own probe core so I can deorbit the booster that brought it up (clean up space). When I go to deorbit the upper stage the orbit of the now larger Moho spacecraft shifts to a highly elliptical orbit that takes the craft thru the planet and subsequently crash my Moho Spacecraft into Kerbin.  Has anyone else had this issue? I was also having this issue before update 1.

[Filed.Teeth]

Yes.

Something as simple as putting a recoverable launcher and payload rocket into orbit will do it for me.

After separation, I will bring the launcher around one orbit to land it back near KSC, and the payload rocket (which is not being controlled at the time) will jump it's orbit, from something in the 70-75km range to having an AP of  ~250km and impacting Kerbin about 90 degrees further along in the orbit.