Unfortunately they are different, the owner is different also, the ftp files have the name of the account as the owner and the group but the files created by php have numeric values for the owner and group.
The server also prevents you from changing the owner (they don't allow use of chown) which means that I can't change the group because I don't own the file.
Interestingly I'd set up seven galleries before I bought svManager and imported them from an external folder. They worked OK and then I needed to relocate everything because I couldn't get the php code for the gallery index to work in my own page.
I renamed the application folder, moved the external directories into it, renamed them to g1, g2 etc, deleted the data file and re-imported them again and I can use svManager and make changes manually because I have ftp access to the folders.
I'm happy with the way its working at the moment, I really need to look at how to customise the gallery index.php file so I can get it to fit in with what I want to do on the site.
I did manage to change the html generated by the automatic index creation php script so I could open the gallery in a new window.