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Hello,

Try starting your computer in safe mode:
Turn on your computer.
Wait until the initial loading screen appears.
Begin tapping the "F8" key. Avoid tapping too soon or you may cause a...

It should be possible to install Spybot 2.x and keep Spybot 1.6 as well.
They have different installation folders and registry key entries.

The recommendation to remove any previous versions is...

When do the popups occur? Or do they appear randomly? Have you checked Settings -> Dialogs -> Immunization? Which Spybot version do you use?