I've played around with container settings and cannot replicate the behaviour you describe. Nor can I think of any reason why the native FM field would not meet your needs. Try creating a new instance of the field and see if you get the same behaviour.
I cannot replicate too on Win7/FM13v2/IE11/AdobeReaderXI.
'Interactive' use 'browser technology' so it depends on OS/Browser/PDF plug-in/and their versions.
There is probability that your PDF viewer plug-in can't open one file in two or more windows. This will cause your issue.
if you are running windows then download latest acrobat reader.