A clogged breather can definitely cause axle seals and other seals to leak. Most seals (but not all) are designed to retain fluid under more or less no pressure. Obviously that's not the case for things like head gaskets, fuel system, cooling system and certain transmission stuff. But for a rear differential, a couple of PSI can cause lube to blow past a seal. The older and more worn the seal, the less pressure it takes.
Also, are you sure the diff had positive pressure and not negative pressure, when you pulled the factory breather? Usually when a diff gets hot, air heats up and escapes from the breather (as you want). When it cools, the breather seals up (small rubber disc under the metal cap) and the air cools, reducing its volume. The result is a slight vacuum. You might have been hearing air rushing in. When I change my rear diff fluid, even with the extended breather, I get air rushing in when I remove the fill plug.
Either way, sounds like you're fine - the seal is fixed and you're dealing with the breather, just in case!
Originally Posted by Eazy.E
Back when I bought my tacoma I had my mechanic give it a once over an he found that my right rear axel seal was blown saturation my right shoes with diff oil. Long story short we replaced the bearing and seal and all was good with the world. I have since had no issues.
So last weekend I had a little spare time and relocated my rear dif breather. When I unscrewed the stock breather a substantial amount of pressure was released. That being said I wish I would have done the mod earlier and left me with the question; does anyone think that a clogged dif breather could build up enough pressure in the rear end to blow an axel seal? I think its possible and could be the reason behind the blown seal in the first place.