Empty tank and remove tank bolts. Dry bottom of tank well. Coat rubber washer on both sides with clear silicone. Reinsert in hole and install brass washer and hex nut. No reason you can't get additional rubber washer and put between brass washer and tank. Also coat it with silicone. Tighten until rubber washers are compressed. I, like everyone else here is afraid of over tightening and cracking the tank. I seriously doubt that you would be able to do that. Especially with a rubber washer on both sides. Sit tank back on bowl and install brass washers and wing nuts.
I suspect that you didn't tighten the hex nuts under the tank tight enough and when you tighten the wing nuts, that pulled the bolts down enough to seal the tank. As the tank sat there full of water for a few days, the weight of the tank and the water put enough pressure on the big gasket around the flush valve to compress it some. That would have made the wing nuts loose. Since the wing nuts, not the hex nuts were what was making the bolts water tight the tank would start leaking.
In other words you didn't tighten the hex nuts tight enough. The silicone will help a lot.