I have noticed this as well. It happened straight after one of the last Chrome updates. It appears google may have changed the default behaviour of the full screen button, or something is bugged out.
If I close down Chrome, the next time I launch it and click full screen, it enters presentation mode about 50% of the time, even though I have never chosen to open in presentation mode. Quite annoying.
I'm pretty sure it's an issue with all versions of Chrome as it happens for me in Canary as well as the stable release.
Only thing to do right now I think is just get used to pressing (control + command + f) each time you start Chrome. My guess is the bug was introduced somehow when they switched Presentation mode to shift + command + f because according to their own documentation that should be the full screen toggle http://support.google.com/chrome/bin/answer.py?hl=en&answer=165450