My skype (184.108.40.206 for windows 7) has started having problems. I'll be having a conversation with someone, and doing other work on the computer. Skype will make its normal beep sound, and that person's chat box will flash. I'll click on it and no message will be there.
I've talked to that person in other chat mediums and they confirm they're sending me messages, and receiving my replies. But their messages are just going missing.
I've tried uninstalling and reinstalling skype, and that did not fix the problem.
Check your computer’s clock time. Has it been wrong in the past?
However, you problem might also be with received messages having wrong timestamp. See e.g. this:
Also you can download this free application - SkypeLogView.
With SkypeLogView you will be able to see all conversations still saved on your computer and verify their timestamp.