As I cannot reproduce the problem and nobody was willing to debug it (as already described here), there isn't much I can do, I need your help with it.
If Skype client isn't sending notifications about the message, there is not much we can do other than downgrading to patched Version 3 or 5 which are still working fine, because there is no official support for Skype API anymore, so we cannot complain to Microsoft and tell them to fix the bug.
For Miranda NG users, I suggest using patched Skypekit, works fine too.
Btw.: I also implemented SkypeKit support into imo2sproxy, if anyone is interested, I can release my version which then also provides skypekit support for Miranda IM.