well, what you missed at Hivelogic is this: the $PATH variable can be  
and is set in more than one dot file.
.bash_login
.bash_rc
.profile

etc...

There can be a precedence for these, based on which one gets loaded  
first or last.
What you need to do is investigate what all you have on your machine.  
You need to check more than just your home directory too. You should  
check some things higher up.
this is all shell stuff, it could be true in any shell, but the most  
common used on OS X is Bash.
I recommend picking up a copy of Unix in a Nutshell. ( you need to  
have a reference like this around anyway and this one is good for  
multiple *nixes )
It has a nice section on Bash configuration, so you'll always have a  
reference of where to look for these things.
sometimes when you install software or  run updates, this stuff gets  
changed.
Usually what happens is another bit of software prefers to use  
something for all *nix systems rather than using what is commonly  
used on a particular system. For example, I installed a newer Python  
recently, and it gummed things up because it created a dot file that  
wasn't there before. This is really a problem with Bash. It allows  
multiple files in multiple places to determine your $PATH all  
together, so it can take a little work to track it all down. The key  
is to get it how you want it/need it all in one file and then comment  
out the stuff in the other dot files and leave a comment of why and  
what it was for, including the date. This will give you reference in  
the future.
Don't be afraid to comment the hell out of those dot files that store  
PATH information. You need it for when (not if) your PATH gets  
screwed up.