I just ran a test here with relative paths lots of them in the project search path and with the “Always use Search Path from Project Settings File” checked and it worked fine. I have reviewed the code diffs between the two releases and the only changes relate to support for the next version of Delphi.
I need more information. Ideally can you send us the dproj file (to support at finalbuilder dot com - or attach it to a reply here). That way I can step through the code and see what is happening.