OK I think I understand the issue. The 3.5mm "headphone jack" is only capable of transmitting 2 uncompressed channels (stereo). The same is true with a pair of red and white RCA plugs.
3.5mm and RCA plugs can carry compressed/encoded streams like DTS and Dolby Digital which allow for more channels as long as the origin can encode and the destination can decode these signals. This is common with equipment like receivers, televisions, DVD players, etc, but it's uncommon for speakers themselves to decode these streams.
Instead, your speakers probably derive the subwoofer channel from either or both of the L&R channels. Meanwhile, your pulseaudio configuration has actually specified a dedicated LFE channel with a crossover frequency of 80Hz. That means that anything below 80Hz is being sent to a dedicated LFE channel, and everything above 80Hz is being sent to the appropriate L or R channel.
Since there is not actually a dedicated LFE channel, the connection is only passing along the L&R channels which only contain frequencies above 80Hz, per your configuration. Everything below 80Hz is not being sent to your speakers at all. All of that lower frequency sound is missing and your subwoofer effectively isn't being used.
You should be able to solve this by changing your config to use 2 channels instead of 2.1. This will allow your particular speaker configuration to work if it is designed to have the subwoofer derive its channel from L&R, as I suspect.
First, back up your config, in case you need to tweak it:
sudo cp /etc/pulse/daemon.conf /etc/pulse/daemon.conf.bak
Now edit the file:
sudo nano /etc/pulse/daemon.conf
Comment out the following lines:
; remixing-produce-lfe = yes
; remixing-consume-lfe = yes
; lfe-crossover-freq = 80
And change the following lines:
default-sample-channels = 2
default-channel-map = front-left,front-right
Save Ctrl + O and Exit Ctrl + X
Then restart pulse with:
pulseaudio -k
