It is not known why, but custom themes destroy the compatibility of homebrew. For example, with custom-themes, you will not start homebrew such as DukeNukem3D or Quake 3. Of course, there are more such applications. In addition, the latest RetroArch Nightly builds have a tendency to crash, where this effect without a custom theme does not occur. So, if you care a lot about Homebrew. Do not use custom themes.