Have you tried running another cable from the L6 link out of the L2t back the Line 6 Link in of the L3t? So that both speakers can fully talk to each other. Above you stated that you only have the L6 link going from the L3t to the L2t.
This will also let you use the two input channels from the L2t and it will act as a single 4 channel mixer with EQ and effects. Plus of course then you also get a pair of stereo RCA inputs on each speaker for a total of 2 and another combi line input on each speaker.
I think the reason the volume might be dropping is because when you are in mono and plugged into only one channel the signal will go to both speakers, when you switch to stereo, it's going to just go to one. Check and see if the master volumes on both are at the centre detent 12:00 position. Are you just plugging in an acoustic guitar?
I just did a quick test with my gear and confirmed that when you put these in stereo mode, Channel one only goes to the left speaker and channel 2 only goes to the right. I also noted that regarding the effects if you are in mono they always work in both speakers. When you are in stereo for some reason some crazy things start to happen.
SO both speakers in mono all 4 channels come out of both speakers. If you have one speaker in mono and the other in stereo then the behaviour depends on mode of the speaker you are plugged into. And again this is with L6 Link running both ways between both speakers with 2 cables. So if speaker 1(L) is in stereo and speaker 2® is in mono, channel 1 of speaker 1 will only come out of speaker 1. Channel 2 of Speaker 1 will only come out of speaker 2. And, because speaker 2 is in mono. Both channel 1 and channel 2 of speaker 2 will come out of both channels.
If both speakers are in stereo mode then as stated above channel 1 of both speakers comes out of speaker 1(L) and channel 2 of both speakers only comes out of speaker 2®. Now when the speakers are in stereo mode only channel 2 effects controls the effects for both channels plugged into that speaker. And the effects come out of both speakers so If you are in stereo and you are plugged into channel 1 and you add some reverb (from the reverb of channel 2) your main dry voice will come out of speaker 1 but the reverb will come out of speaker 1 and speaker 2. The EQ works the same way, if you are in stereo mode the EQ on channel one does nothing and the EQ on channel 2 effects both Channel 1 and 2 of that speaker.
I wasn't able to test the acoustic modelling in stereo mode as I didn't have an acoustic electric handy and the effect is too subtle to hear an effect on a voice.
Hopefully this helps.