When you edit your config, you need to edit the ones that are in custom > my_stuff (or whatever you named it).
If you are changing stuff through you console or in-game tf2 options, the game saves it to 'tf > cfg > config.cfg', which is wrong, so here's what I did to make those changes:
1.) Save '\custom\my_stuff\config.cfg' over the 'tf\cfg\config.cfg' file (this keeps your current binds and other configs).
2.) Re-launch tf2 and make the in-game option changes you want, then close it.
3.) Copy the 'tf\cfg\config.cfg' file and paste it over and replace the 'custom\my_stuff\config.cfg' file.
Check and see if that fixed it. If it didn't or you're confused (cause I suck ass at explaining), then just add me or something.
EDIT: Easier way is what Whoopee_Cushion said. If you find and put all the commands for those in-game options in your autoexec, it'll just set them everytime you launch tf2 anyways.