There are 2 problems with original plug-in and PC EQ, and only one you could not fix yourself:
1) if PC EQ is not in the first position, MackieControl operates whatever module is the first position instead of EQ. My mod suppose to solve exactly this problem (the same for Compressor)
2) the mapping for parameters was changes since original Filter EQ. The mapping is in .INI and in my version EQ and compressor are mapped correctly (also there are 6 strips in EQ3 mode for 6 bands, including HP/LP)
So, put PC EQ in the first position. Switch to EQ mode 2 or 3.
a) if you turn encoders, do the control SOME EQ parameters? If not, your BCF setup is somehow incorrect ("normal" MCU has the display for indication what is going on, with BCF there is no way to see that). It can be that EQ button on BCF is not really EQ button for Mackie or other hardware mapping issues
b) in mode 3, does the mapping looks reasonable? If not, most probably you are not using my INI file
c) if you move the EQ from the first position, does BCF still control it in EQ mode? if not, you most probably are not using my mod
Plug-ins inside FX chains can not be controlled by design of FX chains.
FX bin plug-ins was always (and still are) controllable, including EQs and Compressors in the corresponding modes. But you should map your plug-ins yourself in the INI file, delivered stock mapping (also my INI) has no definitions for up to date plug-ins delivered with Sonar.
So in general MackieControl plug-in with my mod has no known shortcomings. There can be problems with installation and/or hardware setups (especially with "compatible" devices like BCF), but such problems are user setup specific and can be solved case by case.