Funny you mention that, because my gearbox has been out 4 times. Luckily (for me) it was a warranty issue, I bought my '07 TI with a years warranty on the box when I bought it. The noise was there from the start when I bought it last june, but more noticeable during wintertime 'cause the box doesn't warm up that rapid in low temperatures.
I brought it back to my garage and they also pinpointed it as a gearbox-problem. They took it out, refurbished a couple of damaged/pitted bearings, put it back on, the noise was still there. They took it out and apart again, refurbished all the bearings, noise was still there... I'm sorry to say, but they kinda gave up on it after that (€€€). The final thought was it could be one of the shafts that had a little play in it. And they might've been right, because sometimes I could feel an odd little vibration when coasting in 3rd gear.
The story nearly ended when they bought a second hand gearbox and put it on, though that had the typical gearbox bearing whine in 5th and 6th gear. Again... they took it out and refurbished that box completely and now the noise is gone
Big credits for my garage though, for not leaving me hanging. In total it must've cost them near €5000.
I wouldn't know if it's a good thing to drive on with it. I did for nearly 11 months and it didn't get any worse. Most damage was because my bearings were heavily worn, the box had some metal flakes in the oil. That damaged some gears as well. You said you've had the box refurbished already... I'm no mechanic, I've had it replaced in the first place because the sound made my ride sound cheap