for problems cou can make this checklist:
Is there a mxd file generated in the arcgisoutput directory?
yes, is there generated the desired output file in the same directory (pdf, png, ...)
yes, is the file accessible by the arcgisout url in a browser winwos
yes, try to debug the flex part, the SOE is working fine
no, check your webserver settings
no pdf, there is a problem in the export part. Check the AGS server logs in verbose mode
no mxd, the is a problem by interpreting the JSON part to configure the SOE. Check the url which is send to the SOE or maybe post it in the forum. I will take a look on it
Tom