Ghost peaks and elevated baseline

I am using GCMS 8890 with a 7010B TQ system. We ran into an issue with loss of sensisitvy and had to clean the ion source. After cleaning the ion source we have been running the samples after restoring the sensitivity.
However, we are running into a new problem with the elevated baseline. It happened all of a sudden as I was running some samples with Haloacetamides (HAMs) in MTBE, we started seeing huge unidentified peaks and elevated baseline. We baked the column to fix the issue, but the issue persists. I've replaced the rinse vial, rinsed the injection syringe with fresh MTBE, ran a fresh MTBE blank but the issue persists. I am attaching here some images for your refenes:
This is what the Uknowon Analysis looks like for one of the blanks I ran:
And these are the two chromatograms for two subsequent blanks that I ran, it seems that the problem is getting worse. 

And below is what I ran today, after baking out the column again:
The tune reports are looking good. Looking for possible answers, suggestions, and steps to solve this problem. 
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