I wonder if it's not rebuilding the index for the textures somehow.

This is the line of code from ha_mfd.c that assigns the texture.

mfd_texture_screen = create_system_texture_screen (mfd_texture_size, mfd_texture_size, TEXTURE_INDEX_HAVOC_TRQ_GAUGE, TEXTURE_TYPE_SINGLEALPHA);

The TEXTURE_INDEX_HAVOC_TRQ_GAUGE refers to the index in textname.h. In the IDE, it resolves as 2318, which relates to the index. But maybe it's not rebuilding the index. I'll try adding some logging and see what happens. If I change textname.h and run a dmake build, it doesn't show anything changing. If I run remake, then dmake, it rebuilds everything again, but hasn't fixed the MFD display.