The thread pitch for the aftermarket Brembo M/Cs are 1.0, while OEM is 1.25.
That's odd that your Fren Tubos aren't installing properly. Normally this happens with Galfer and Goodridge lines because their banjos are thinner, in which case you'd have to use their banjo bolt (with proper thread pitch) in order for it to fit properly.
I have Fren Tubo Type 4s on my 09 R1 with a 19RCS and it fit properly, but I have a Ti banjo bolt. Can't remember if the Ti banjo bolt had the same specs as the Brembo bajo bolt though.
After doing some research on the R1 Forum, some members on their doubled up on crush washers. On my 09 R6, I doubled up on washers with the Galfer brake lines. Current set up is: Bajo bolt, two crush washers, left brake line, one crush washer, right brake line, two crush washers, 19RCS M/C. I haven't had any issues with it so far. Wish my bikes were here with me, otherwise I'd post some pics. Mind you went and bought new crush washers prior to install.
Edit: Here's one thread from the R1 Forum - http://www.r1-forum.com/forums/showthread.php?t=296084
You can even file down a few threads on the Brembo banjo bolt if need be.