I'm not able to reproduce your problem because I don't have a configuration file for my remote and WinLirc.
However, I might have a solution to your problem : girder.
Girder has the same function as winlirc, but is far more powerfull and easier to train.
I wrote a small tutorial about remote controlling BSplayer over here :
http://users.skynet.be/RafkeP/tutorials/remote/
It's a little outdated and covers both WinLirc and Girder, but I think it's a good place to start.
For version 1.0 and above of BSplayer, use the following gml file :
http://users.skynet.be/RafkeP/tutori...yer100.805.gml
I did a little test and girder does not show the problem you report.
Feel free to contact me in case you have more questions about this.
Good luck,
Rafke P.