After market KNN. I just put in a new filter.
K & N can cause issues just waiting to happen, if you search issues with K & N on a Duramax you'll find a lot, same issues as your having.
The big problem with K & N is its only 4 layers of media which allows more airflow than the stock MAF calibrations allow.
More airflow going thru allows the oil to easily get sucked thru as well which causes MAF problems.
This is critical and easy to over oil these filters causing your issues, oil with caution.
With your tuning probably changed the MAF to allow a little more airflow, when you took out the tuning you also decreased the maf calibration.
I've known several that had no issues at first with K & N refused to believe me that they will, usually within one year they start having these problems, the filter thins out oil easily gets sucked thru.
They offer a sock for these filters which would reduce the flow a little and maybe trap some of the oil.
One thing to consider (and this is fact) K & N oil will destroy the MAF sensor especially if it gets on it and burns.
AFE oil will not destroy the MAF (self proven and claimed) or cause issues like your having, I will only use K & N air filters on NON turbo engines the additional airflow being pulled thru from a turbo with a K & N doesn't hold up very good.
I only use AFE oil on all of my aftermarket airfilters.