The "Verify saving assets" option is useful for catching cases where the TFS Plugin silently fails to check out modified content. Unfortunately, having this option enabled exposes bugs in Unity where settings files are unnecessarily overwritten, resulting in extra wasted time dismissing popups.

Repro Rate: 5/10 - 50%

1. Launch Unity 5.1 editor
2. Click Edit -> Preferences
3. Make sure Verify Saving Assets is checked
4. File -> Build Settings
5. Set configuration like this:
Platform = Windows Store
SDK = Universal 10
UAP Build Type = XAML
Uncheck all three boxes
Click Build
6. Select HoloStudio's checked-in WindowsStoreApp directory as the build target
7. Build

Result: Annoying dialog pops up most of the time
Title: Save Assets
Text: Unity is about to save the following modified files. Unsaved changes will be lost!
File: ProjectSettings/ProjectSettings.asset

If you look at the diff of the ProjectSettings.asset file, nothing is actually changing from the checked-in version. This looks like a case where Unity engine code is aggressively dirtying the in-memory settings file state despite no actual changes being made.