PTC reads multiple files to load options, such as mapkeys. You may have removed it from one config.pro, but not from other locations. There are several config.pro files in different locations.
Open the Options. There is a view that says Current Session. This should be the top of a drop down that lists all the files that are the source of current options. Change from one to the next until you see the mapkey you are interested in, which will tell which file you need to edit.
To make things easier, create a separate file called mapkey.txt. Then move all the mapkey definitions to that file. Finally create a mapkey that loads opens the options using mapkey.txt and store it in config.pro. Any new mapkeys can be saved in mapkey.txt; PTC appends the mapkey definitions to the file.