I am by no means an expert, but I would suggest you do the following at the end of your MIOS_Init() (assuming you’re doing this in C, otherwise you will have to do the likewise in asm).
Loop through all your AIN pins, grab the 7bit value and transmit MIDI accordingly.
so the pots aren’t at the position they are on the software…
… do you really want that?
The Position of your MIDIBox Pots have no meaning to the position (timeline) of your DAW project.
Assuming you open another project: Your position of the pots is wrong but the PlugIn setting stored in the DAW is how you left finishing the project the last time you worked on it. If the MIDIBox sends now the actual pot positions to your DAW, your PlugIn settings are way off of what you want to hear.