During initial setup after the first site is created it copies skins from the library at /Data/skins to /Data/Sites/1/skins (1 is the SiteID). If it timed out during this process it may have failed to copy some files in which case it will fall back to a fail safe skin.
I recommend copy all the files manually from /Data/skins to /Data/Sites/1/skins to ensure they all are there.
Hope it helps,
Joe