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Are you clicking save after you have checked the box? And depending on what anti-virus software you use, could have an effect on stopping skype from running on startup.
Have you tried completely removing Skype and reinstalling?
If that doesn't work, the other thing I have noticed is you have to have both Start Skype when I start Windows and Sign me in when Skype starts (Located on Skypes Sign in screen) checked.
I found the cause. I have an app called Soluto installed. One of its goals is to speed up boot time by allowing you to decide which of your apps should start in boot and which can be delayed or paused. I had Skype delayed and it seems that doing that undoes Skype's option to start with Windows. By returning it into boot via Soluto it now starts normally.
Thanks for your assistance in any event Beowolfv!
After installing Skype, I get a blank Skype logo and blue sky background. What do I do?
Look here for an appropriate solution.
Be careful with selecting the correct procedure corresponding to your Windows system and the version of Internet Explorer.