Reaper gets media with identical filenames but different subdirectories mixed up

Steps to reproduce:

1) Make a new project
2) Under project settings, set a path to save media files.
3) Make some media files in that audio path.
4) Make a subdirectory under the audio path.
5) Put files in the subdirectory with the same name as the files in the root audio path.
6) Put the files from the subdirectory into your project.
7) Save, close, re-open

The items will now be using the media files from the root audio path rather than the subdirectory.

Noticed this with a project where I was using a subfolder of my audio path to store all my post-melodyne vocal takes, and the items kept reverting to the pre-melodyne takes whenever I closed and re-opened. Reproduced with a brand new blank project.

EDIT: Forgot to mention, the audio path should be relative.

EDIT 2: Project in which this bug can be easily reproduced:

http://analogy.cupofnoodles.com/reaper/filenamebug.zip

The files under /audio/ohai have the same content as the files one level up, except their names are swapped.

In the project, I have two tracks which should be using the /audio files, and two tracks which should be using the /audio/ohai files. If you inspect the .rpp with a text editor, you should see that the track "Arglebargle 2" is using the audio file "audio/ohai/02-Nerfherder...wav", and oppositely with the "nerfherder 2" track. However, if you open the project in Reaper, it uses the identically named files from under /audio and not the files from /audio/ohai. Try adding the files from /ohai to the project, save, close and re-open.