the newly-electrified traces probably accelerated the electrolysis effect on the ones that had the goo trapped underneath the solder mask. So, i would start checking crappy looking vias/traces. 

I see this all too often. Go good after recap shortly fail because the current flowing produces the electrolysis effect on the goo that remains behind even after a wash. 

I had hapain send me the same mac portable board 2 or 3 times before I finally got it right.