The mamewah.ini isn't finding your new layout so it defaults out to the standard one.
I have this:
mamewah.ini = 
layout                      jking_cabthen I created a 
jking_cab  folder
saved a layout as 
layout.lay  in that folder
background image is named 
main.bmpFor my VirtuaNES layout, I created a file 
virtuanes-main.lay within the jking_cab folder.  Now it switches with the different emulators.  It has a seperate background image 
virtuanes-main.bmpIn my case, the layout.lay and main.bmp is the default setup for the jking_cab theme.  Until I create emulator-main.lay and a corresponding emulator-main.bmp, newly added emulators will use that default setup.
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I haven't sorted any ROMS yet, I have an idea I'm going to try... 

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Snapshots have to have the same file name as the ROM they represent.  I'd guess since you're seeing some of them that it's a naming issue.  ie:
"abcd_123.zip" needs a corresponding "abcd_123.png"