This is a known issue, and we are currently investigating possible solutions.
The workaround requires you to delete all categories/cost codes that reference the lower case version and reenter with upper case. A chargeable file fix could be used as well if you have many entries already posted to them.
Note: Depending on your needs you may determine that it is easier to change the original contract value on the Contract Item>Contract tab. This will have an effect on the Original value and the Revised value and may be sufficient for your reporting needs.