Most waterproof fabrics are have the waterproofing layer bonded to the inside of the fabric so it won't easily wash off. On the outside of the fabric there is usually a non-wetting agent and it is this that washes off.
You can tell if this layer is still active by dropping some water on. If it soaks in*, the layer is gone. If discrete drops form, then it's still working.
There are wash-in and spray on additives to reactivate the surface. I've used both but I now stick with the spray on since they seem more effective.
These days I hand-wash my waterproof gear in Nikwax and, after a thorough rinsing, I spray it with the surface treatment then leave it to dry.
If you wash the jacket/trousers etc in the machine, it's important to run the machine through one or two empty cycles without detergent (hot is good as well). You need to remove the traces of the conventional detergents otherwise they will take off the non-wetting coating.
If your knees are getting wet in your trousers then there could be several reasons for this:-
- pressure is exceeding the "withstand" pressure of the coating forcing water through
- the coating is damaged
- it's not water getting in, it's sweat condensing on the inside of the fabric because it can't transmit through the membrane fast enough
*All other things being equal though, the water shouldn't go through to the inside of the fabric.