Possible causes:
1. Gap limit. Electrum has a default gap limit of 25. If the other addresses are past this generation limit, Electrum won't see them until you force it to.
I think this is the most likely reason for OP's issue, @OP can you confirm?
I suspect OP reused his main receiving address, and change amount goes to change address
as many times he did this, new change address also created that many times
and possibly past 25+ addresses gap limit, so electrum not seeing the rest of his coin in that change address