New FTP user creation procedure on the one particular domain takes a long time. FTP user modification on the same domain goes very slowly too. On other domains these operations goes without delay.
Check the number of the files at the domain directory. Most probably the httpdocs directory contains many files. Operations with FTP accounts require setting up permissions on the files. If there are too many files, it will took much time. For increasing the speed for operations with FTP users, decrease the number of the file in the httpdocs directory of the domain.