It's likely due to the system thinking you're a different user and that those files were associated with the old user. If you can ssh into the system with putty or a similar program find the offending folder and run as root:
chmod -R 777 /your_folder_path
That will make the folder and all files within it have read,write,execute for root, all groups, and all users. I wouldn't do something like that on a PC running linux but should be pretty safe on a gaming handheld. Also, I'm not sure what username the newer firmware uses during normal operation, but if you found that out you could run as root:
chown -R the_username /your_folder_path
That would solve the problem with less of a "security issue". This simply changes the owner of all of the files to the username provided but doesn't change permissions.
