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On line 535 of the downloadable uncompressed version of popcorn.js Popcorn.util.toSeconds does not pass this.options.frameRate as a second argument.
The same is true for line 594 of the exec method.
EDIT: There are actually multiple calls to the toSeconds method from within popcorn where it doesn't pass the frameRate option and in addition to that, there are places where "framerate" is used instead of "frameRate"