This is something I saw in PADs 9.5 and now again in VX2.4.
If you have a placed part on a schematic and you alter the library symbol such that you keep the same names but update the pin #, when you do an "Update Symbols" the symbol's parameters update EXCEPT for the pin numbers. I'm not sure why it works that way or if there is something in my methodology that is broken.
The way I've worked around this is to remove and place a new symbol down. Sometimes doing a "replace symbol" works, sometimes it doesn't so I've tended to error on placing a new symbol, updating any parameters (VALUE, PART_NUMBER, REFDES) to match the existing part on the schematic and deleting it. I only have been doing that on parts that I know the pin numbers have changed.