Hey Simon,
Did you upload the configuration via the upload configuration command or tftp put?  
If tftp put you essentially have uploaded the configuration as a xml file.  If you used the upload config command you are uploading as ASCII.  
XML format you can tftp put the .cfg file to a switch and run the "use configuration " command.
However, if you uploaded the configuration as a ASCII format you would need to save this as a .xsf file and download to the switch.  Once in the memory "ls" you should see the file with .xsf extension.  At that point you must run the command "load script " Then save the configuration.
Let me know if you have any questions.