There is a workaround to this issue. To understand the workaround, it'll be good to understand what's going on with the bug a little better.
So the issue with this bug isn't with loading or saving configurations, but rather it is with switching between them. It seems that when switching between two of the same thing (for instance, two Mobile Application configurations) it doesn't properly clear the data out of the form, and since the form isn't cleared out it doesn't properly load the new information in and as such the old information carries over. And since the save code still works fine, when you exit it will save the new, messed up configuration over the old, good configuration.
So, technically, it's not the same configuration showing up twice, but rather two separate configurations that are configured the same because the form didn't clear out when switching between the two configurations.
So now that we have a clearer understanding of the bug, here's the workaround: If you click on something that uses a different form, it will destroy the form. So, for instance, if you have both an iPad Simulator and an iPhone 4 Simulator, and you've got the iPad Simulator selected and you need to select the iPhone 4 Simulator, simply first click on Mobile Application, and then click on your iPhone 4 Simulator. When you do this everything works fine.
Additionally, if you do switch directly between the two, know that the configuration that you just left is fine. It's only the one that you're currently looking at that is messed up, and all that you have to do is fix the one that you're looking at.
So that at least let's you work around the issue. It's also convenient to just set up enough different configurations to where you never really need to access the Debug Configurations menu. For instance, I have have two configurations set up for each device or simulator that I have set up, one that has the 'Clear application data on each launch' checkbox checked, and one that does not. In addition to this, I have four simulators (iPad, iPhone, Android Phone, Android Tablet) and one 'On device' (Android) setup. Combining these gives me ten different configurations that covers majority of what I do regularly and makes it so that I don't need to access the Debug Configurations menu all that often.
At this point with this many configurations it is also useful to organize all of these configurations in the debug dropdown menu by using the Organize Favorites menu that can be selected from the same dropdown menu.
So, that makes for a very long answer, but hopefully it will help you out and help out a few other people that are also running into the same issue. It doesn't change the fact that there's a really horrible bug and that Adobe really needs to get on fixing it, but this can at least make it so that it can be lived with.
Perfect workaround! Thank you so much. I can now get my device configurations to "stick".
It is a nasty bug, yet simple at the same time. Hopefully Adobe will see this post and make a fix...though my hopes are not high on that unfortunately.
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First, I apologize for touching an old thread, but I found a better workaround and I figured that it would be good to add it here in case anyone needed the information.
So this bug is run into when going through the 'Debug Configurations...' option in the dropdown on the debug button or run button. There is another location where you can edit the device configurations that does not have this same issue. If you go to 'Project'->'Properties'->'Run/Debug Settings' then you can edit all of the same information here without the risk of losing your information because of the bug in Flash Builder.
I hope it helps someone out.