I have Windows 7 Home Premium and I do not experience this same behavior anymore, although some of them did cause some headaches. If you can get a distribution of python that has compiled .exe wrappers for the power-tools, I would try to do this (I never call pip.py, I have a pip.exe that executes in cmd.exe right out of the box).
Most notably, take care when executing .bat files that wrap up your scripts. BAT files will do what you described if not set up properly. Instead of using BAT files, I prefer to make links. Then you can set the target manually and other execution characteristics.
If you are having trouble with a particular command, you will probably need to track down the actual target of your command, and see how it is being run. Some pythons wrap up modules in .BATs, and they can behave wrong if you don't realize this.
One last thing, running commands from the Run-Prompt IS NOT THE SAME as running from cmd.exe. I don't know the exact differences, I just know that it generally does not work.
If you are in cmd.exe, and you type 'python', what happens?