page 18 of the manual (FTP user guide - 1056.pdf) ;-) gives details of how to include characters like %, @, ; etc. in the command line by releasing them.
it works fine for us - but as the release characters (%25, %40 etc.) contain % you may have to be careful if you are using the Resource Registry. The Resouce Registry will replace anything between two % so you may have to replace the release characters too - let me know if I've confused you this!
Cheers,
Olly.