I haven't been able to reproduce this on my end... and I just created a new account at Planet-Save and entered one password using the right-click > populate, and the other with the 'Copy to Clipboard'.
One thing I did remember when doing this that you may not have noticed...
When you use the 'Copy to Clipboard', you have to open the PM Settings...
What you may be missing is, there is already a password generated, and you *can* copy it to the clipboard - WITHOUT ENTERING YOUR MASTER PASSWORD - but if you do this, the password will be different than the one that gets populated from the right-click, because it prompts you for your Master Password. I actually ran into this myself when I first tried to use PM...
If this isn't the problem, have you guys tried testing with a clean profile and fresh install of the PM extension?