I've carried out some trials in this area so I'd be interested to find out
what the problem turns out to be in the end. One q I'd put to the fab house
is wheter or not they removed the unused innerlayer pads on one PCB & not on
the other, the unused pads definitely improve the life expectancy of the
vias in my expierence. If space allows on your designs it would be
benificial to increase the annular ring on the inner layer signal vias, this
will help reduce the number of hole /pad breakout instances & give the hole
a 360deg anchor point on each layer. 
As other posters mentioned the copper thickness in the hole walls is also
important 1.2 -1.4mil if possible.

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