There is likely a bank of dip switches on the side and only certain bills are enabled.
It should be an easy change.
One reason to disable $50 is that apparently you could take $5 and using a pencil could make a few marks that the validator would then recognize as a $50. When people asked the Casio why they could not use $50 they were told they were unlucky.
Subsequently when the new money came along - I believe the $10 was the first the casinos who were still using S+ (and not willing to pay for the s2000 upgrade) simply disabled the new monies. I believe the colored $5 was the last bill to be released and JCM was never paid by IGT for it and the firmware for the validator was never officially released. Somewhere along the line it did make it out into the wild and has propagated.
The new dbv series never had the sensors to support the new magnetic bills.
On another not some people set the dbv denomination to 1cent so a $bill quickly puts on 100 credits.