The plugin system is not designed for the mobile display. I mean any defined header or footer plugins should show but the mobile templates do not have the hook locations for the obvious reasons. There is no sidebar there is no thumb display on photo display. There is no profile page. All the areas really the hooks are shown in the regular display do not exist in the mobile display therefore no areas to show content. You can edit your mobile templates and add in any hook locations you want but we do not support that.
There are only 4 plugin locatins I think that would be valid in mobile header and footer should work as I stated. The majority of the locations like I said would not be valid since they would not exist.
The header and footer plugin locations should work on mobile.
The only locations that could theoretically be enabled on the mobile would be top of bottom of the category display page and top or bottom of showphoto page. There are not alot of locations because most stuff is now shown on the mobile display. it is severily limited which is why the header and footer are really the only ones active.