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I'm not sure, whether it's a core Winlirc problem, or an issu with IRToy plugin, but there is a problem.
Some Pioneer remotes use double codes like
Same as Sharp Protocol.
WinLIRC is able to decode Sharp infrared signal to 2 parts hex number.
In order to remote control a Sharp device, both Normal and Inverted signal must be transmitted. But transmit.exe only transmit the first part.
My work around is manually create Sharp remote config file in rawcode format.
The trouble with IR protocols is there are so many, and some differ in widly different ways. The sharp protocol is one of those strange ones that fits outside what LIRC will recognise. The raw method is what I would suggest, but looks like you are already doing that. You can try asking on the lirc board to see what they say about this protocol.
I found out the cause of this bug, I will try and address it in the next release :)