De acordo com o Wine, o login no Skype for Wine não funciona. Você deve editar seu arquivo Skype.desktop
:
[Desktop Entry]
Name=Skype 7 Wine
Exec=env WINEPREFIX="/home/.../.wine" wine C:\\Program\ Files\ \(x86\)\\Skype\\Phone\\Skype.exe /username:"username" /password:"password"
Type=Application
StartupNotify=true
Comment=Launch Skype 7 Wine
Path=/home/.../.wine/dosdevices/c:/Program Files (x86)/Skype/
Icon=4F0B_SkypeIcon.0