[ronie]

I added with EMM some dummy files that correctly showed most media flags (I always get one or two blank boxes, studios?)

yep, most likely studios since not every studio logo is included.
others may be subtitles and/or mpaa rating, if the info is not available the skin can't display a rating icon.

Now after deleting this source from the library I enabled "Extract metadata" in the Video Settings of the skin, it went and added media flagging to my files in HDD (.mkv, .avi, .wmv..) but it also show "DVD", "blu-ray" (I don't have a clue how it assigns these flags since the name is "clean")

if there's no tag in the filename, the skin tries to 'guess' the source by looking at the file-extension and resolution.

I didn't like that so I disabled the option, reload the skin, restart XBMC but the flags are still there!! I cannot get rid of the dreaded DVD/Blu-ray logos

I wonder if there's some kind of bug with the "Extract metadata" setting and Transparency! does not disable it correctly.

the "extract metadata" setting has little to nothing to do with showing media flags in the skin. the "extract metadata" option will scan your files and store the data in the database. in case your using .nfo files with tags in the <streamdetails> section, xbmc will always read those, no matter if the option is enabled or disabled.

if you want to hide the mediaflags in the skin:
Settings > Skin Settings > Icons > **** - Show media flags