Right now the texture matrix is only applied when ENTITY_GLINT is defined. This causes some texture issues with the physics mod.
Turning this (located in src/basiccoords_vertex.glsl):

#ifdef ENTITY_GLINT
  texcoord = (gl_TextureMatrix[0] * gl_MultiTexCoord0).xy;
#else
  texcoord = gl_MultiTexCoord0.xy;
#endif

Into:

#ifdef ENTITY_GLINT
  texcoord = (gl_TextureMatrix[0] * gl_MultiTexCoord0).xy;
#else
  texcoord = (gl_TextureMatrix[0] * gl_MultiTexCoord0).xy;
#endif

Or:

texcoord = (gl_TextureMatrix[0] * gl_MultiTexCoord0).xy;

would fix the issues.

Thank you for the correction. The proposed fix (and similar tweaks elsewhere in the code) has been implemented in version 8.6g.