This is not a bug in mojoportal, this question would have been better posted in the Design and Skinning forum.
Sounds like you are not updating the correct file for the child site. Skins used by the site are located under /Data/Sites/[SiteID]/skins so skins are isolated for each site.
Note also that if you make a mistake in editing the layout.master it can cause an error and fail to load your master page in which case it will log the error and load a failsafe master page. So if you think you are editing the correct file you should also check the log under Administration > System Log to see if it is logging any errors related to your master page.
Hope that helps,
Joe