This appears to be working in our tests, but you may be seeing an edge case that we missed. It may help for you to include some screenshots of what you are seeing in an email to omnifocus@omnigroup.com.
(You can take a screenshot by pressing command-shift-4, which will give you a selection cursor. Tap your Space key, click on the window you want to capture, and when you release the mouse the image will be saved to your desktop as 'Picture 1', 'Picture 2', etc.)
You can then drag the images to an email message and send them to us. We'll use the information they contain to try and figure out what's going on here.
(You can take a screenshot by pressing command-shift-4, which will give you a selection cursor. Tap your Space key, click on the window you want to capture, and when you release the mouse the image will be saved to your desktop as 'Picture 1', 'Picture 2', etc.)
You can then drag the images to an email message and send them to us. We'll use the information they contain to try and figure out what's going on here.