Quirks in opening upgraded SL2 file uploaded in LMS

I have noticed several quirks in the files that were built in SL1 and later upgraded to SL2.  Most of these (font and animation changes, submit button additions, etc.) I have corrected, but when I publish the files for LMS, they are launching two windows: a separate IE window that is blank except for an orange "launch" button in the middle, THEN the module window.  

When originally published, these modules worked fine.  Also, modules built exclusively in SL2 perform correctly.  Can anyone help troubleshoot this?

Thank you!

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