You seem to have come & gone multiple times (with absences of unknown length) from Korea. I recommend that you contact the NHIC
directly (as you have already done once) and explain your situation clearly (the number of times that you've left & the duration of each trip outside of Korea). Only then will you get an accurate answer.
To the best of my understanding: YES. IF
ALL of your trips out of Korea were less than one month in length each, then the date used to assess the 3 month wait period would be your initial date of entry.
I hope this helps.
