@PaulineC There's a limit to what the RRF config tool can do, and one of the limits is that it doesn't do custom motor mapping with more than one motor per axis (yet). You can define the Duex; on the 'I/O Mapping' page, click '+ Add Duex 5', and this will give you the option to use the outputs on the Duex. But you can still only map one motor per axis.
Because you added the motor mapping on the end, it meant that those motors did not have their motor settings (jerk, accelerations etc). The M584 command that maps motors to each axis needs to come before this. If not, the motors will usually use default values, but I'm actually not sure if this applies to motors connected to the Duex.
Anyway, glad it's working now!
You may want to update the WiFi Server firmware, and Duet Web Console (DWC) software, too, as I expect yours will be old versions. To do this, upload the following files from https://github.com/dc42/RepRapFirmware/releases/tag/2.05.1 to the sys folder on the Duet:
DuetWiFiServer-1.23.bin
DuetWebControl-SD-2.0.7.zip
When uploaded, these should ask you if you want to install them. If not, send M997 S1 to update the Duet WiFi server, and M997 S2 to update Duet Web Control.
Ian