ultra micro auto main line grow

so after last week the plant took a slight turn for the worst, to begin with at the end of week 2 it had filled out the solo cup plant pot with roots far far quicker than i expected, and 3 days after repotting into a larger one it still wouldn't perk back up.. somehow the water runoff from the larger pot was quite acidic with a ph of around 5! I dont understand how as it is the same soil and water as the smaller pot it was in and the water ph was around 6.1-6.5 from the smaller one. I had flushed the soil as much as I can and the runoff is now around 7 ph but I don't know if it will become acidic again later on and now waiting for the soil to dry out as it has probably overwatered the small plant by now, however it is still growing just far slower than it should be.