LH and FSH are released by the pituitary... TRT does not change their level (mine were completely the same before and after), and nor does reproductive tissue atrophy (where both Estradiol and Progresterone will cease endogenous production from those tissues). And they're actually not merely for 'feminine things', critical for males as well.
I'm pretty sure the switch to IM is going to help with this on it's own. Most often, this will linger when your dosage is inappropriately LOW rather than high. Basically, Estradiol and Progesterone AND Testosterone plummet to start it and then rise to stop it (but with Progesterone lagging to peak in-between; it's predominantly responsible for the thickening of the endometrium - and it itself can be effective in skipping sharkweek by pausing the cycle in that stage indefinitely; however, it isn't good to mix exogenous Progesterone with TRT. Clotting risk is too great, most doctors will not prescribe both simultaneously for that reason).
So, providing you're at a high enough level of T (TT 300 or greater; levels that induce reproductive tissue atrophy), this really ought to not still be happening.
Otherwise, I think you should discuss also going with a WEEKLY administration over the typical bi-weekly. The more stable your level remains, the better - and it surely will help with this issue as well. And, as I know full-well it can get rather more sore to inject IM weekly in the same general areas, you can and should also ask about SubQ.
That all said, if this is still going on after the switch to IM (say, 3-4 months)... then I'd think that would be grounds for an ultrasound. According to my Endo we're supposed to have one of those yearly (prior to hysto/oopho) anyway. You might have fibroids (etc.) causing this.