When an electronic file is sent to the iGen [or other digital presses], it is seeing the swatch names. Even if a Pantone swatch has been converted to process, if the swatch still says "PANTONE 285" or "Pantone Red 032", the iGen is picking that information up and using its own color look-up table for that swatch regardless of any mix or alteration you may have made to that swatch.
If you do convert a Pantone spot to process, be sure to rename it, such as "285_4cMix" or the percentages like "22.214.171.124".
Above is a screen shot, showing a file with Pantone 285 and Pantone Red 032 converted to process, altering the color mixes dramatically, but still keeping the original swatch names. In this case, changing Red 032 to a blue mix, and 285 to a red mix. The resulting printout from the iGen is that what is red on my monitor prints PMS 285 Blue, and what is blue on my monitor prints Pantone Red 032.