Thank you for your post.
I have sent your comments to our Development and Testing departments for review.
As a workaround, have you considered just selecting the window instead of using Open URL? I'm trying to determine why Open URL is necessary for the related file.
Testing was unable to replicate the issue on both Mac OS X 10.9.5 and Mac OS X 10.10. An extra window only opens for the first time when you go back from File B to File A, and after that, no extra windows open. Global variable are present.
Are there specific steps used? Do you have sample files that we can test?