Matrex seems to forget the Project settings (threading, etc.) after a restart;
This was caused by Matrex not being able to overwrite the project file.
The files are the following (in alphabetic order):
matrex_1_3_7_generic.jar for any platform
matrex_1_3_7_linux_gtk.jar for Linux
matrex_1_3_7_macosx_32.jar for MacOSX with 32 bits Java (Java 5)
matrex_1_3_7_macosx_64.jar for MacOSX with 64 bits Java (Java 6)
matrex_1_3_7_win32.jar for Windows
The bug has also been fixed in the code of the next release, 2.0.