There is a question about stack overflow on similar lines, but the question concerns only one element. The project in this case was created for iOS2 and the new version of Xcode was used. This led me to review the latest builder interface release notes (3.2) that say:
"Interface Builder documents can no longer be saved in NIB 2.x file format. NIB 2.x files will be automatically updated to NIB 3.x files when opened."
So, I suggest you check the file inspector of your nib files and check their current version. I suspect Interface Builder is simply trying to update 25 nib files to version 3.x. If you have older files with the Carbon filter, see the Xcode Release Notes (v.4.0 - current) as they require the use of version 3.2 in Xcode 4 and later.
Xcode 4.6.3 displays nibs version control in the file inspector using the following menu items: 
So far, Xcode 5.0.1 is slightly different version versions.
The project document should also be in the latest format:
.
The basic premise is that Xcode converts the project file / nibs at boot time. If this repeats on every boot, I would report it as an Apple error at http://bugreport.apple.com . I think the information found indicates the correct problem. Verifying that the files are using the latest version should fix the problem if no error is found.
Other things to try:
- Upload the project to a separate directory / directory (there may be some corruption on your current one)
- Start the console and logging as the problem occurs (you also need to record system logs for Apple, but the console may display a useful error message)
References
- What is the interface Builder Cocoa Touch Tool, link .
- Xcode Release Notes (version 4.0 - current), link .