"I had the same problem with Vista SP2. I used the same trick for when the Microsoft updates got stuck:
I deleted everything regarding Skype from the hosts.
Navigate to the following location:
Windows 95/98/Me:
%Windir%
Windows NT/2000/XP:
%Windir%\System32\drivers\etc
Windows Vista:
c:\Windows\System32\drivers\etc
Double-click the hosts file. If necessary, deselect the “Always use this program to open this program” check box. Scroll through the list of programs and double-click Notepad. When the file opens, delete all the (Skype) entries. Save."
"When installing Skype 4.1, its base library Skype4COM.dll (version of 2009) is being stored in ?:\Program Files\Common Files\Skype but old version of Skype4COM.dll (of 2007) had been stored in \Windows\system32. After disabling startup of the new version, Skype starts by means of old library. The records of both libraries are in registry at HKLM\Software\Microsoft\Windows\CurrentVersion\SharedDlls (all listed dlls run at Windows startup, old Skype4COM.dll runs as if disabled Skype).
The method of curing:
Exit Skype Delete both records from ....\SharedDlls key Restart in safe mode, delete old Skype4COM.dll from system32 Restart Windows (Skype must not start if it was diasbled in settings) Run Skype manually and set option ""run at Windows startup"""
"I have been searching for an answer to this for ages as my Skype stopped autolaunching with a 2017 update, so although this is a slight variation to the question (it's a different version of Skype and for Wimdows 10) this was the ONLY thread anywhere that I found that dealt with the problem so am posting a solution here for others still looking (ironically most other results were for how to STOP Skype from auto-launching!) The link below shows you how to add apps to the start-up folder in Windows 10:
