Ah! Unfortunately this sounds familiar. It is possible that you've caught a virus or you are breathing/sleeping with your mouth open now that you have the trays, but it is also possible that you are responding to the chemicals that were on the trays after they were manufactured.
Most people have no problems with this sort of sensitivity, but I did. It was very uncomfortable. Now, I thoroughly wash each tray with toothpaste and tons of fresh water before using it. If you have yet to really thoroughly clean the trays you are wearing (some orthos suggest using water only, but other cleaners like mouthwash, vinegar, and toothpaste work well without issue and get rid of the residue), I suggest you do so. I am so sensitive that I cannot use conventional mouthwash, but if you use something you are already accustomed to, it should work like a charm.
In the meantime, drink a lot of water, especially at night. To me, water is the most important "medicine" available. Your body will flush out any toxins from the trays, and your body will also benefit from the added hydration. Almost six months into treatment, I still drink water all day long - lots of it! Since I started cleaning the new trays before wearing them, I have had no problems.
Good luck, and feel better!


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