Steps to reproduce:
In a folder, execute this in a folder of your choice:
mkdir -p bug-st-project/test/myfolder
ln -s test/myfolder myfolder-link
Then create a project in Sublime Text and add the bug-st-project to it ("Project" menu - "Add folder to project" entry)
Check the folders on the left sidebar and unfold test/myfolder. You will notice that the test.css doesn't show up whereas it does in the myfolder-link folder.
The test.css only appears in the myfolder-link folders and doesn't appear in the test/myfolder folder.
Ctrl-P - typing test.css doesn't show twice test.css.
The test.css file should show up both in the test/myfolder and myfolder-link folders.
System : Linux (didn't try on Mac OS X so far)