With my usual quip out of the way, I think your interpretation is up for discussion. Are weapon magic enhancement bonuses a core part of the weapon? If they are a core part, then the current behavior is correct. The wording on Vital Strike is like most weapon based wording which assumes the + of a magic weapon is inherently part of that weapon.
Actually the wording
on Vital Strike is quite different from every other feat. In fact is the only one feat (or one of the few, anyway) that explicitly mentions "dice". And since it's one of the most controversial feats in Pathfinder it has received a ton of errata, some of which from Jason Bulmahn himself. Here's something taken straigh from the FAQ
of PFSRD (in turn taken from the Paizo boards):
Q: The text of this feat stipulates that the Vital Strike does not multiply Strength damage, weapon ability damage, or precision damage. Are other damage bonuses (those not mentioned, such as those from Weapon Specialization, enhancement bonuses, or the Bard's inspire courage ability) are, in fact, multiplied on a hit? I'm not sure if that's what is intended, though--the wording sounds like it could just be saying, "No damage bonuses, such as X, Y, and Z, are multiplied on a hit. "
A: (Jason Bulmahn) The way to think about it is this: roll the damage dice only twice
I hope to not sound obnoxious... it's just that I've done my homework
Oh and the news of the new version of your framework is both a blessing and a curse: many new features (that attack frame makes me drool) and so many customizations that will be lost!