There are several different possibilities, I'll list all I can think of.
1. Your not saving your file in the right place, hit save as, and save it manually to where you want.
2. Wherever your running it from is the wrong file, check either WED or SED (wherever your running it from), and find where it is running the script from, once again, manually set it to the right folder that you have "save as"ed
3. Your opening the wrong file, I'm guessing somehow you've duplicated the files to have very similar code but one it outdated, the other is not. Find them both (hint hit save as, wherever it brings you is where your saving your file) the other one is wherever you've been selecting it from. Delete one so you only have 1 available, if you want more then one copy, save it as a backup and put it in an out of the way place.
4. Besides restarting your computer to get rid of any temporary files that might be screwy I'd suggest going through the list 1 more time to make sure you've gotten it all.