Waterproof treatment for trail shoes

Tiger:
You are correct that the goretex should have protected you from a leak. Given the way you describe the leak at the toe, is it possible that your pronation has caused a hole to rub in the goretex on you toe (inside the shoe) that you can't see outside? A waterproof treatment may help some, but I would not suspect much at this point. Did you put different insoles in the shoes? Sometimes these can rub the goretex liner and cause a hole, but usually this is at the rear, near the heal. not sure there is much you can do now.
As to smell, washing would help, but then you should be vigilant to let the shoes air and maybe pu foot powder in them to reduce the smell. I found that after each day, if I pull the insoles out and stick a piece of newspaper in each shoe, it would make them dry. If no newpaper is available, just let them air.

Hope that helps some.
Rambler

Goretex works by principle of vapour pressure. The only way its waterproof is if you can seal your foot in the boot. It works well enough to prevent water from entering the boot if you wade through a puddle. It won't work if you wade through a field of wet grass ... nothing works for that. It could be you are expecting too much of the boots.

Meindl sells boot wax for its footwear. Its highly recommended that you treat your boots with it or products like nikkiwax or even mink oil. This stuff helps the waterproofing qualities of the boot.

Waterproof does not mean watertight.

Goretex increases the rate at which shoe funk builds because they don't dry as quickly or as completely as a non-waterproofed. The moister environment inside a waterproof shoe more rapidly gows the bateria that are the source of the funk smell.

About the only way I know of really knocking back the funk bacteria is with an extended soak in an enzymatic cleaner like Resolve followed by a quick wash. Detergents can be problematic on GoreTex, so you may need to do an extra rinse or two. Regular detergents and washing won't eliminate uthe bacteria base.

The enzymatic soak is also good with other tech fabrics that can develop an otherwise permanent funk after a while. I will sometimes soak them overnight.