This is a known issue in Skype 3.6.0.248. Follow instructions below to turn the tray icon pink again.

1. Double click on two black arrows in main Skype window (left bottom corner).
2. Click "Disconnect" (link in right bottom corner of the Pamela entry as identified by Pamela.exe).
3. After that icon will turn pink again.

We have reported this to Skype and they are looking at this issue.