When I Alt-right-click on a button to edit it, the Customize dialog box always appears and most of the time is quite annoying.
Is there anyway to prevent it from popping up when I edit my buttons?
No, there isn't.
(As it is currently, if the Customize dialog did not appear then you would have no way to exit Customize mode and save (or cancel) your changes.)
You can turn on the Minimize Customize dialog option; then Customize will open minimized and it will close again automatically when you finish editing the button.
I stand corrected. I forgot that option even existed. Have just turned it on myself. 
That sounds perfect! How do I turn on the Minimize Customize dialog option? I've searached through the preferences and through the customize dialog box itself to no avail.
Use the filter field in the bottom-left corner of the Preferences dialog to locate it.
Thank you Jon for pointing out the filter box. I instantly found the Minimize Customize dialog option. I will use that filter more often!
[quote="nmccamy"]Thank you Jon for pointing out the filter box. I instantly found the Minimize Customize dialog option. I will use that filter more often![/quote]I must say that for a program with the huge number of preferences offered by DOpus, the filter box was a brilliant innovation. It's disappointing that the concept has not been widely adopted by others.