CHM files use Windows that are defined. You do have access to the settings for the window that govern how it behaves. I'm happy to share where you might check this. But odds are that you will discover it's not the CHM and any configuration setting it contains. Likely it has more to do with the manner in which your application developer is calling the CHM. I believe in the help call itself they are able to specify the behavior. If you want to confirm this, just open the CHM on its own by double-clicking it. If it isn't above other apps, there's your proof.
To verify the window settings, click View > Pods > Project Set-up. Then expand the Windows folder. There you should find a window definition for your CHM file. Double-click it to open the Window editor. When it opens, click the Advanced Properties button in the lower right corner of the dialog, Then click the Extended Styles tab. This option is titled Top-most Window.
As I said earlier, my guess is that you will find this isn't enabled. But it won't hurt to double-check it. As a last ditch effort to prove it's not the CHM file, you can try defining a totally new window and configure that window as the default when you compile. And if after all that the CHM *STILL* is on top, it's time to toss it in the developer's lap.
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Thanks for the suggestions Rick.
I think the main issue was corrected in the View > Pods > Project Set-up area. There was one window that had Top-Most Window enabled, so I made sure that the option was off in all for all of the windows and it does work a lot better now.
Now the Help can go behind other programs except for the application the calls it. I guess I'll have to forward it onto a developer at this point.