Great feedback there and no I don't think you're imagining it at all.
I had a feeling you might find something similar but didn't want to say anything to prejudice the evaluation.
Without taking anything away from the JL, I suspect the primary reason for what you're experiencing with the SVS - a sort of detachment from the Kefs - is input and DSP processing lag. As well as being a fantastic package, with an industry leading driver and quality amp, the JL has the advantage of having a very short signal path. It really is lightning fast thanks to all those factors. With the SVS it gets a little more complicated, whilst the DSP is a welcome feature for many I really do think its adding enough of a delay that you can notice it with direct comparison against a top flight sub like the JL. The only way to level the playing field so to speak is to add a delay to the Kef/main speakers. However this will require added complexity to system such as the addition of a miniDSP like device or audio processor unless you're using the analogue preouts from the PC where you can do it within the software/audio driver. Even then I still think the JL would have it.
Yes I think there's something to this, though I don't think it explains all of the difference. In addition to this I think the JL Audio is more nimble too, that is to say that the drivers are better able to start and stop movement more rapidly leading to better reproduction of sounds that are short and intense like certain types of drums.
With the SVS I felt like the note played for a bit too long and sounded rounded off (in terms of its length not its frequency response). I didn't get that with the D108.
So let me caveat the rest of this by stating that I have certain sensitivities to sound, I quite like loud music but I am very intolerant of any distortion or things just not sounding right. Sorry I can't explain that better... but please bear this in mind in reading what I write below. For most people its quite possible that what I say below wouldn't be true at all. I haven't yet met anyone who had the same kind of sensitivity and aversion to distortion the way I do.
Right, so the rest of the afternoon I decided not not try and listen critically but just put on a playlist I've been listening to recently and then listened to it first with the SVS and then with the D108. During this I wasn't trying to pick out differences between how the two subs sounded or anything. Just see which one I enjoyed more. The playlist I was using is about an hour long, and a mixture of EDM, House, Techo ish type music with overtones of various ethnic mixes thrown in (bit like that Ilios track I referred to but more varied). Selected not for its bass notes, but just because I've been listening to it a lot recently. This was all done while sat at my desk and working too so not focused particularly on the music.
When listening with the SVS after a few tracks I felt like turning off the music, or more accurately just turning off the sub. I didn't, because I wanted to keep listening to see how I liked it overall. When I got to the end of the playlist though I did turn off the music for a bit and left it off. Actually one other thing I should mention is that when I first plugged in the SB3000 Micro, I instantly heard some coil whine. I was pretty close to it at the time and I wasn't sure if it would be a problem, but when the music stopped I could still hear it. Its at a very high frequency and very faint, so I imagine most people won't even hear it, but I found it annoying.
I then swapped over to the D108 and put the same playlist back on. This time however I found I was tapping my feet and just engaged in the music. I didn't feel like turning it off, in fact I often turned it up for a bit. When the playlist ended, I just put on a different one.
Sorry that's not a more technical analysis of how they perform, but for me that I think it is enough to make pretty firm decision on buying the D108.