Sussambs idea is a good one. In my case I just filled my boots up with water and left them overnight. Really annoying in the morning when you can see water around and along the external seams!Took a while for them to dry, but they did and in three boot cases I've taken them back, either to be refunded or to buy another brand of boot.
I have also had wet feet for the other reason, I wear gaiters and the trouser fabric above the knee became wet and the water seeped down between the gaitor and trouser fabric, into my socks and of course from then on I had wet feet.
I have now more or less solved this problem, I now wear my gaiters under my trousers, not necessarily perfect, it depends on the type and intensity of the rain but its much more effective that my previous way of wearing them.
Even though you were wearing waterproof leggings I still believe that in certain weathers and rains water can travel upwards, over the top of your boot, into your socks and then wet feet again. I believe this happens because when we are walking the bottom hem of the trousers may move, swish back and forth and send the wetness upwards. I always noticed that in some wet weathers, or when walking though long wet grass, the inside bottom of my trousers were often wet up to about 2" sometimes. I've seen this clearly when I used to motor cycle to work, on arrival how did the rain get down inside my wet weather gear? I always noticed that at certain speeds as the rain hit my chest area, some flowed downwards but some flowed up, over the top of my tightly fitting neck area and by the time I got home I could be soaked from from neck to groin.