I'd say that it is due to the effect of raising your T3 dosage, which suppressed your TSH, thus no longer stimulating your thyroid gland to produce hormone, which is actually progress for you. Serum thyroid levels are the sum of both natural thyroid hormone and thyroid medication, so with a drop in output of natural thyroid, the increase in T3 med did not have any effect on FT3 level. Only after TSH is suppressed will further increases in T3 med start raising levels of Free T3.
Since your thyroid levels will now be totally due to thyroid med, you will probably ultimately need a T3 increase of approx. 25 mcg to get your Free T3 level into the upper third of its range. Assuming that your doctor is willing to continue to raise your med dosage as required to relieve symptoms, you should try to get back to see him soon and ask for further increases in your T3 med.
What are your actual Vitamin D, B12 and ferritin levels?
Your TSH is already suppressed, so it won't change much. Anyway, it really shouldn't have have any impact on decisions about your treatment. Our bodies evolved with continuous low flow of thyroid hormone, When taking adequate thyroid med in only one or two doses during the day, the equilibrium among TSH, FT4 and FT3 changes significantly, with TSH becoming suppressed for an extended period from the relatively large amount all at once.
When taking thyroid med, a suppressed TSH does not mean hyperthyroidism unless there are attendant hyper symptoms due to excessive levels of FT4 and FT3. So don't let your doctor tell you that you need to reduce your med dosage because of the suppressed TSH. Instead, with the symptoms you are still having and your FT3 at rock bottom of the range, you need further increase to get your FT3 into the upper third of the range, or as needed to relieve symptoms.
I should have added that your ferritin needs to be at lest 100, so an increase in your iron supplement is also needed.
I think the higher dose of T3, will make you feel great! (Ok nobody with thyroid issues is great- but lets say better!) I had been on just T4 meds for 17 years...still never feeling right. (Not sticking with testing, forgetting my meds..) So tired, ALL the time. Finally Dr suggested the T3 & T4 meds...I am feeling 10 times better! It takes time though- give it a couple months. But stay on top of that testing!! Couple of things- ALWAYS keep thyroid meds in the FRIDGE! A very, very smart Immunologist told me that... I never thought my meds "worked". Guess what- they work great if kept in the fridge! Also, empty stomach, same time everyday. Get full absorption!!