I too had a lot of problems with this program but once it work its great!
A the problem y foun are all related to not having the same name of device in all the apropiate files, AND THIS INCLUDE THE DEVICE NAME IN THE DEVICE FILE ALSO!
so you have to have the file name ok in the lirc con, the remote file, the device file, AND inside the device file in the device name.
i have a remote with 2 devices and it works ok so for mi is not a problem.
Also remember you can generate new devices with lirc on linux and with winlic on windows, youll just need a cable plugged in an audio port, line in, or com port. Ive used one ir receptor from a pc tv tuner i had and it worked ok! so i can generate all the remotes i need exactly.
hope it helps