Are you instructing Spybot to scan on startup? Or is Spybot attempting to remove the entry on bootup because removing it was not possible during the Windows session?
Go into Spybot » Mode » Advanced mode » Settings » Settings. In the options tree scroll down to the Automation » System start. Click on the "No automation" option (both the "Automatically run program at system startup" and "Run program once at next system startup" should then be unselected).
When you're done it should look like this:
├─ System start
│ ├─ ● No automation
│ ├─ ○ Automatically run program at system startup.
│ ├─ ○ Run program once at next system startup.
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