There appears to be a bug that causes new contracts to be generated with fund rewards after save/loading without fully exiting the game application. It can be fixed by fully exiting the game before reloading a save.
Steps to produce:
1. Start KSP with Bureaucracy installed
2. Start a new game
3. Test contract generation -- newly generated contracts work properly, replacing any fund rewards with reputation
4. Save game and exit to main menu
5. Reload game (or start a new game) without exiting the KSP application
6. Test contract generation -- any contracts generated before save/load will still have fund rewards replaced with reputation. However, refreshing the contracts list via cancellation, completion, or waiting will generate new contracts which have fund rewards
7. Save game and exit the KSP application entirely
8. Start KSP again and load the save (or start a new game)
10. Test contract generation -- as before, any previously generated contract rewards stay as they were before exiting. Fortunately any new contracts now generated will be working as desired, with reputation in place of funds
I have reproduced this behavior with a fully fresh installation of KSP, running only the Bureaucracy mod and its requirements. It also appears when other mods are installed, such as contract configurator and the exploration contract pack, or when installed in my full modpack.
If you're still interested in updating your mod, this would be a good thing to fix -- I thought the mod was irrecoverably broken before I managed to pinpoint the exact behavior. If not, this post can at least serve as a guide for how to avoid this issue for anyone else facing it. Simply exit out of the main menu before reentering your game and everything will work perfectly.