Famitracker looks for the "plugins" directory relative to the processes current working directory (which is normally whatever directory contains the FTM file that I double-clicked on from Windows Explorer).

Famitracker should instead use the win32 api "GetModuleFileName (NULL, ....)", then strip the EXE off with "PathRemoveFileSpec", then append "Plugins" with "PathAppend" (or at least, that is how I would do it).