Adding on to @HelesicPetr , what's happening is you are creating a new drawing in a workspace but your config.pro is pointing to a local folder for the default formats. Creo will retrieve this file from that local disk and it will appear new in the workspace. But that same format filename exists in PDMLink which causes the conflict. I would recommend keeping official copy of formats in Windchill. You will have issues with folks working in and out of the system but you can export formats to that same local folder so they retain the Windchill parameters in that file. I think that helps.
What we did to solve this problem is commit to Windchill where the config.sup points to Windchill exclusively.
pro_format_dir wtpub://PDMLink/Libraries/Engineering CAD Resources/Formats
This path points to the library where our formats exist. The key to this is all users must use the same "name" for Windchill in their Server Manager. This can be accomplished by scripting the initialization of server connections for the user. We've had no issues like this since.