My opinion.. it isn't a software problem, it is a development management problem.
From the little I have seen and researched of YAF.. being open source like they are and being IMO poorly managed as a collection.. they introduce code that is constantly stepping on other elements of the code.
Common issue with a wide range of coders compiling into a single source.. but over the course of PH run on the software, it appears that they are not learning from their struggles.. they are cycling them over and over.
I was caught in a ERP rollout nearly a decade ago with similar problems, it wasn't until the company rebuilt the development strategies and became more rigid in the development standards and processes that the software improved. Eight years later, the company has gotten the process refined into a very solid and fluid company.
Eight years.. but it took constant improvement over the course.. something that IMO, YAF isn't doing at this point.
I don't know their overall structure, but IMO, that is the root, not the language the platform is built upon.
"The oranges are dry; the apples are mealy; and the papayas... I don't know what's going on with the papayas!"