All was working fine, then while making unrelated changes and on next build came across the same issue. Used source control to compare to previous versions and discovered that my ../Content/Scripts folder had mysteriously been emptied!
Restored ../Content/Scripts/*.*from a backup and all worked well!
ps: Using VS2012, MVC4, had recently updated some NuGet packages, so that might have played some part in the issue, but all ran well for a while after the update, so not sure.