Waiiiit did removing Twilight Forest SOMEHOW fix it?! When you went exploring was it in Twilight Forest? If so I know exactly what the Bug might be.
Go into your Save File, and look ad the dim7 folder, the one containing Twilight Forests Region and other Files. Are they absolutely HUGE for no reason?
Specifically the “/saves/yoursavefile/DIM7/data/TFFeature.dat” should never be in megabyte territory, if it is in the dozens of megabytes THAT is your Lag Source! Luckily it can be safely deleted as it regenerates just fine. I have not encountered any issues after deleting it early on during my own Twilight Forest Save, which I later finished the TF Progression on entirely without any related bugs popping up.