More than 7 hours to save a project

I am using DVD Studio pro 4, and my project has more than 1000 menus; the file size is about 5 GB. When I make a few changes and hit “save", DVD Studio Pro is taking more than 7 hours to save the project.
I know more than 1000 menus seems a bit unusual, but we are an authoring house, and we develop training DVDs with hundreds and sometimes thousands of screens.
Any suggestions on why DVD Studio Pro 4 is taking so long to save the project?
Note:
I am using a G4 with OS X 10.4.8, dual 1 GHz, 1.5 GB SDRAM of memory, and my project is on an external 500 GB Lacie hard drive.

Thanks for the responses. I really need to get this problem resolved.
The changes I make usually involve adding more menus and assets to the project.
I do have the setting set to "Auto Assign Buttons Continuously." However, I imagine if this were a problem, then it should affect the response time of the application when it is being used, not after one hits "save". I really need this feature, and I would hate to have to change it.
I am not using templates; I am using my own menu assets--a different graphic for each menu. And all of my assets are in a "graphics" directory that is in the location as the project. The external hard drive has 245 GB free space.
What do you mean by the following?
"DVDSP writes out the file information every time you save"
Thanks.

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Luis
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More than 7 hours to save a project

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