Very good question.
I've only tested this software with the Sky3DS linker with the blue button, I've tested it lots of times, don't worry, that works perfectly.
However, I haven't got the Sky3DS with the red button, I can't say you if this software works with this linker.
If you have got the Sky3DS linker with the red button (and some time to lose) and you want to test this software to know if it works, thanks in advance to share me your results... ;)