I have had both and had them built with the exact same parts... and put many miles on both of the frames. They were both nice bikes but a little different with pros and cons to each
I ride the large frames in both - The SIR9 weighed 4.99lbs with the eccentric installed, the Jabber 5.01lbs with the jabbernutz installed, both on the same scale one right after another on the same day...
The Sir9 rides a little smoother, however the bottom bracket is not as stiff. You get a little sway back and forth when standing... nothing severe, but noticeable. The Jabber rides a touch rougher, but the bottom bracket and headtube are MUCH stiffer than the SIR9 - climbs a lot better.
The Jabber handles different than the niner - you really need to test ride both...but depending on your preferences, this may be a good thing. The Jabber freaking rockets downhill... the bike is very stable and the stiffness in the headtube area helps. the niner steers a little different as mentioned above... really this will end up being personal preference.
The warranty on the SIR9 was great. I actually had 2 SIR9's and 2 One9's when I was riding the Niners. I broke multiple frames in the time that I rode them, and niner always replaced them no questions asked. Kind of a pain, but they took care of each one in a timely manner. I have yet to break a jabber frame - I have one going on two years that is still going strong with no issues whatsoever...
Also, the other major thing is chain tensioning for SS use. The niner uses the eccentric, which worked well but required a lot of maint to ensure it did not creak. I would get creaks every 4-5 rides unless I cleaned it out. The EBB worked great (actually, it worked better than I was expecting!) and was easy to adjust or add additional chain tension.
I really really like the dropouts on the Jabber. I thought they were going to be a nightmare when I got the bike however it is just the opposite. Super easy to adjust, change gears, and no noise at all. You have to use a really good skewer (crank bros split works awesome) to avoid the wheel from moving, but it is worth it. I am also lazy, so I just change cogs without adjusting the brake

FWIW, I have an optimus TI with the Paragon sliding dropouts, and I prefer the dropouts on the Jabber!!
I really liked both bikes, however I ended up liking the Jabber a little better after riding both so I sold or gave away my Niners (made my mechanic happy!!) and ended up riding Vassagos for the past couple of years... even managed to make it on their team!