Visual Studio breakpoints break in the wrong source file (or multiple files simultaneously) if multiple files have the same name
If no better alternatives exist, you could put the breakpoint in code:
System.Diagnostics.Debugger.Break();
Just don't forget to remove it afterwards...
I'm so glad I found this post, thought I was the only one and was going insane! I'm having the same problem in VS2012 with VB.Net and have tried everything the OP mentioned.
Unique naming of the files seems to be the only 100% fix that I've found. Disabling all breakpoints until the application has loaded and then re-enabling the breakpoints you need works most of the time. Breakpoints in Lambda functions can still give you issues.
I just had the exact same problem. What solved it for me was deleting the .suo files belonging to the solution that contained the affected project/source file.
I also deleted my local symbolcache but I don't think that had anything to do with it.
(My solution contains multiple projects, one file (DataAdapter.cs) in one project was affected by this (VisualStudio put my breakpoints in the pdb belonging to System.Data.DataAdapter). I opened the .csproj file directly and was able to correctly set the breakpoint.)