Ah, how silly of me - this occurred to me less than minute after I posted. To fix the weighing problem, just make it impossible for component editor to screw up: make it re-weigh against every joint by unlocking the weighting on all joints.
This is what I used to fix my misbehaving vertex:
string $thisjoint;
string $alljoints[] = ls -type "joint"
;
for ($thisjoint in $alljoints)
setAttr ($thisjoint + ".liw") 0;
skinPercent -tv NameOfJointThatSucks 1.000000 skinClusterName MyMesh.vtx[1625];
Not sure when exactly this "bug" kicks in yet, but on a side question, anyone got a good alternative to Component Editor for a numerical weighting tool?