I've stumbled across this one and it took me some time to figure it out. That error will crop up if you are deploying a file either via a feature or site template twice. In my case I had two Modules in an elements file to split up the Preview images from the actual files being deployed to the masterpage gallery. that's where SpVisualDev gets its knickers in the twist. Can't deal with multiple modules in one file and keeps on adding all files to the last module. also the ones that are already referenced in the first one.
Fix? put all files into one module or SPVisualDev will screw with the elements and it won't work.