I'm attempting to get eclipse running as something more powerful than a colored text editor so that I can do some Maya scripting. There's literally nothing fancy about this setup, it just doesn't keep my interpreter once the prefs window is closed. 
I can open and view .py docs fine, but pydev will not keep the interpreter I give it. As soon as I save the prefs with vanilla python.exe chosen as the interpreter, eclipse loses it. Opening the prefs again will show a blank interpreter page. 
Auto config used to work before I started mucking with settings. I had the same disappearing problem even though Autoconfig could find everything. 
c:\Python27 is set in my PYTHONPATH for user and system variables. 
I've tried 32 and 64bit python (running win7 64). I was using Aptana with pydev and it seemed to not complain for a while, but then the interpreter went awol and I tried Eclipse to fix it. I can't start an actual project due to the missing interpreter, and the large "help" box that pops up when I'm typing is slowing me down considerably. 
Eclipse 3.7.2
Python 2.7.2
Pydev 2.5
Thanks for your help, I'm pretty green at this.
I had the same issue. This is how I solved it:

Go to your workspace folder.
Edit the file ".pydevproject".
Change the path located after "PYTHON_PROJECT_INTERPRETER" pydev property.
Save and you're good to go.
Eclipse + Pydev wont keep interpreter setting within the same session.