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Value of Popup menu in GUI is different when I Load it than when I Save it.

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I have a large GUI with above 700 handles in it. When I save the GUI using hgsave, everything seems normal. When I open it up, however, a set of popup menus (5 of them, all the same) load up differently than they were saved. No matter which of the three options it was supposedly saved as, it will always load up as option #3 now.
I've tried tracking down the problem and have narrowed it down to what I think is a small region. I've checked up until just before the save command within hgsave (line 268), and everything is still fine up until this point.
On the other end, I have checked the handles immediately after opening the saved *.fig file. Regardless of whether I open it normally (as a functioning GUI) or in GUIDE, the values are changed.
I do have some lines of code that are designed to make this particular change IF a certain other action is done to a different part of the GUI. However, this action should not be called while opening the figure. At this point, I think something is happening to inappropriately call this line of code (with default values in other handles, perhaps) while the figure is opening, but I'm not familiar enough with how a saved GUI figure opens to properly debug it.
Any thoughts on how I can make the GUI I load the same as the GUI I saved would be greatly appreciated.
Regards, Jeff
MATLAB Version R2009b

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