When you see the status "Last seen days ago" for a Skype contact then you know there's trouble if you spoke to that contact recently. Your messages to that contact will be delayed by 20-30 minutes while he can send you messages instantly, making chats awkward.
This problem annoyed me too in recent months, but I stumbled on a solution: if you send your computer to sleep then always exit Skype first. If the computer goes to sleep while Skype is running then next time you awake it the "Last seen days ago" bug usually occurs.
So the solution is simply this: always log out of Skype before you sleep your computer.