I'm using WP 3.0 Multisite, NGG 1.5.5 and DM 0.5.2, last version of each.
If you deactivate DM's option "Redirect administration pages to site's original domain", in order to keep frontend and backend under the site's domain, NGG's Flash uploader won't work properly.
I'm using Google Maps integrations, so because of the API key I couldn't afford to have that option activated.
I managed to fix this editing site options at Super Admin/Sites, and setting Domain, Siteurl, Home and Fileupload URL to the site's domain.
I don't know if this is actually a bug, but I thought it was worth mentioning.