Do you have invisibles turned on? cmd-opt-I turns them on and off in Illustrator on a Mac.

Sometimes, when I open a file before the fonts are open some of the characters switch to other characters. I've found that I have to restart Illustrator to remedy it.

I've learnt through the years that if Illustrator has a problem it's usually related to fonts. Try quitting Illustrator, trash the preferences, turn the font off, turn it back on, relaunch Illustrator and see if that fixes it.

Also, if your swatch pallets ever go missing in Illustrator it's (probably) because there are a) too many fonts open b) there is a corrupt font open. You could try turning off a couple of fonts you don't need active while you're at it before you relaunch Illustrator and see if it helps.