Looks like a new alpha is out, now up to DSOrganise 2.7 alpha 3 on Dragonminded's blog. One of the changes was a fix to a problem where files or directories might be corrupted when created, so now things are probably safe.
so now things are probably safe.
Yeah, It creates this damn folder called 'DSOrganize' and I can't open or modify it at all. It just kept giving a file corruption error, but afterwards I ended up having to Reformat my card, as it wouldn't even delete.