In my opinion it is more like a simple ink incompatible issue. Nothing was changed but the ink. It does not make sense that it is a color management problem since nothing else but the ink is changed.@mikling may know the answer to this question for my Pro-100.
Why must I set Intensity to -15 using Precision Colors' ink vs Canon?
I am an amateur not a pro. I got my Pro-100 9 months ago and got my ink from Hobbicolors on ebay. I refilled my CL-42s without bothering to flush the carts. I can not be happier by the beautiful result I have got so far.
Try to make everything as simple as possible for troubleshooting. Are you sure nothing in the setup is changed? If no it has to be the ink that messed up.