Yeah, that's a big mistery ...
What I do know:
* Your Sub connector on the main board also has Center speaker on it.
* What software are you running for the soundcard? If it's a soundmax, or Realtek, the software settings can do weird things to sound and how/where it is output to. Maybe try and run without the software running?
* Check the Windows sound settings...
* Splitters do not really work well on these types of soundcards, I've tried several of them, and they do make channels go missing, in my experience.
(As if the onboard soundcard checks/sees what is connected, then adjusts its output to it... I'm not really sure.)
In the end, I have connected some wires directly from the SubWoofers's speaker to an amplifier, that has its output to my butkicker....
In the end, I have gotten myself a Roccat USB headseat, that has connectors to a standard 5.1 speakerset, same three outputs as on onboard sound.
Now, I press a switch on the headsets' controller (sitting at my desk) and I switch between headset and speakers/butkicker.
Finally I've found something that works consistenly (Surround Soundcard via USB) and with which I can easily switch between headset and speakers.
Still, every now and then, in IL2 there's big differences in sound output, different per a/c type (to be expected) but also every now and then, differences in engine volumes, and output to the kicker.
(I blame modded sounds for that, still would rather have stock sounds... and told tell me I can switch those on via GSGME, they are definitely not the same as stock....but, that's a different topic, sorry.)