Just found this out the hard way.
If the costing method for each site does not match what the defaults are part detail screen then it does not show in the stock status report.
To fix, adjust QTY to 0, set all to the same, ADJ QTY back in.
I have a feeling that playing with Non QTY bearing on a site changed to costing method to Std which was not inline with the two sites at AVG.