Tool/software: Code Composer Studio
There's a problem with Program Mode Compilation reproducable starting from at least CCSv5 to CCSv7 (checked myself).
If source files are located at the same directory, program mode compilation work, if creating sub-directories, or adding more source directories - it doesn't.
Compilation works normally without 'program mode compilation' option enabled.
Adding source locations to 'paths' in CDT doesn't help.
Note1: I've found the same problem existed in CCSv4.4 and wasn't resolved due to: https://e2e.ti.com/support/development_tools/compiler/f/343/t/98506
Note 2: I cannot share my project, but this bug can be reproduced easilly.