There is a similar question, but I tried changing audio settings.
I'm using Ubuntu 9.04 and sometimes when talking to specific person it just doesn't send messages or receive them. It may even show that person as offline for few seconds (even if she/he is not).
That may not depend on the other side, because it happened on Windows and Ubuntu box.
There is a possibility it's not really limited to Skype and it's more of a wider problem, I'm not sure.
Best Answer
I'm pretty sure this is a long-standing bug in multiple successive versions of Skype for Linux. In my case my messages are delivered only when the other party sends messages to me. There used to be a thread about this on the Skype Community Forum, but unfortunately the forum has been discontinued with no archives available.