I came acrosss this bug since it describes exactly my problem - except that I can rule out any hardware fault.
My setup is working fine under Ubuntu 12.04 with Kernel 3.13 and LIRC 0.9.0. I installed Debian 8.5 on the same machine on another partition, using the same lircd.conf and getting exactly the problems that are describe above. I am using kernel 4.6 from jessie-backports. I too have a One4All remote, namely URC-6440. I would be glad to help solve this problem, as it is a real show-stopper.
