The format of the weapon table has been altered greatly, to allow for new features (such as beam capable fighters), but the actual specifications for the weapons have not changed. As the file checking will most likely simply perform a CRC or similar, it won't be looking at the weapons themselves, but the 'shape' of the files as a whole. As the 'shape' doesn't match, it's a bad file (sit! DOWN! ohhh, errrrr... not that kind of bad...).
So validator on the server needs to be updated with the new 'shape' of the file, so that it will recgnise it. This would need to be done anytime there is a revision to the table made by the SCP, which may happen if there is new feature implemented...
edit - To Clarify - The important thing to bear in mind is that the tech room has no relation to the actual damage the gun does, therefore, the SCP Kayzer at 10, and the Retail Kayzer at 6, is immaterial, and should not be used to make judgements on game balance issues - only the table can be used for that.
The SCP tech room having different values is effectively a typo that has no in-game effect. Look on it as PR from the manufacturers (Now washes whiter then wh... Wha? It's a Gun?... errr, just say it's more zappy then!), but it's not 'cheap' as it's the same stats. Perhaps the GTVA got sold some counterfeit Kayzers, like overclocked Athlon 2500's being sold as 3200s!