I wonder who and why wrote this, but it is even VERY annoing:

aModule->m_LibRef = aModule->m_Reference->m_Text;

It was copying placeholder for RefId (say, R*** or so) to pattern id (say it was RESC2012X55N)...

pcbnew/librairi.cpp

@@ -160,7 +160,6 @@ void WinEDA_ModuleEditFrame::Export_Module( MODULE* aModule, bool aCreateSysLib
     if( aModule == NULL )
         return;
 
-    aModule->m_LibRef = aModule->m_Reference->m_Text;
     fn.SetName( aModule->m_LibRef );
     fn.SetExt( aCreateSysLib ? ModuleFileExtension : ModExportFileExtension );