same thing happened to me with my txs top mount and my gfb bov. I got the top mount, and not only did the bov flange not fit on the intercooler, but the intercooler cam with some metal shavings in it. Gotta love attention to detail. Anywhoo, I ended up shaving some of the metal off the bov flange and off the intercooler so the bov would fit(with a dye grinder, a dremmel would work though). If you don't wanna do the grinding yourself, you could call turboxs and ***** till they grind it for you, or get a machine shop to do it for a few bucs.
On the note of calling turboxs... We have the same intercooler(I dunno if mine was a version 3 or not, or if there is a version 3 ) and different bov's. I'm pretty sure turbxs knows whats up with bov's not fitting on their intercoolers, unless it's just our two intercoolers. Here is an old post that I mentioned my experience in....
Who's Running TXS/Hyperflow TMIC?