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Well I'll be darned ... that was exactly the issue. I used red PLA because I thought it would stick out nicely to have a red flag (actually does). I had also printed a flag in black PLA so I used the black PLA one to test if it tripped the sensor and low and behold it trips it but just crossing a small amount of the bottom of the sensor arms. I also have another red one that I printed and tried that and inserted all the way into the optical sensor and it didn't trip. Not sure if it is the translucency or the fact that it is reflective, red or something else. I will have to take off one of the X-axis at some point but I currently have a small piece of electrical tape over the flag that is doing the job for now. Thanks for the advice!