It wouldn't shut off like it normally would, the fan would run at a lower speed, and I could feel some vibrating in the machine. Additionally, it wouldn't deliver air like normal after it got into that strange new behavior pattern, when I'd inhale, I could feel and hear a vibration in the airflow. A couple times it was making the wheezing noises that so many have complained about.
What I finally figured out is that the new filter was getting sucked down onto the opening, so it was causing a lot more airflow resistance. I popped open the filter cover, while it was acting weird, noticed the filter was sucked into the opening, pulled the filter out, and the airflow picked up to where it always was before when I'd take the mask off, and then smart start shut off the machine, just like it is supposed to do.
playing with it more, I found that if I put the filter in the square opening of the filter cover door, it would get sucked into the intake, If however I sat the filter in the opening of the housing, and then closed the door, it would pinch the bottom edge of the filter in place, and the filter would stay, and the machine would work fine.
I guess pictures are in order.
How I thought I should put in a new filter:

What happened:

What worked:

There needs to be a little more support around the actual air inlet when using just the thin hypoallergenic filters, but pinching the filter in the bottom of the door seems to be working for the time being

There needs to be a little more support around the inner opening,