The problem is definitely not the boot. It is the combination of the boot and binding. Some just line up at that point. I have several pairs of bindings that I ride with the same boot. Only one strap does this. A different strap is a likely solution.
So if the Burton strap doesn't fit, maybe contact Rome ask for a set of this season's 390 toe straps, which are open in the center and can be capped properly.
It looks like the 2011 390 has a flat strap designed to wear over the toe, which unfortunately has the compressing effect on the soft Vans toe box.