Hormones and Bitches! If you figure that out you can figure out anything!
Taking those pups away (just having pups) defiantly affects there hormones and hormones effect EVERYTHING from mood and drive and depression to you name it.
Working them out does help stabilize the endocrine system wich controlls hormone levels. (especially sprinting for hgh and testosterone) If you have the patiance it will probably correct itself.
If not breed her again and let her raise the pups before you knock em in the head and that will balance them out.