Hello,
this is a potential bug report: I'm currently working with different configurations for contracts, hence I have different contract.uploader.json files in my conf/ folder.
It seems that the contract manager only accepts the standard setting for that configuration parameter, which is "contract.uploader.json".
In case there is no such file with that name, it copies the default one with the example contracts. The file set in the config nxt.properties is ignored.