I am currently on a double entry tourist visa which expires November 6th. Yesterday I went to immigration to get my first 30 day extension (no problem). In my passport it states this ( to keep your stay permit re-entry permit must be made before leaving Thailand). What does thos mean that I also need a re-entry permit prior to leaving to activate my second entry.

That would only be needed if you wanted to leave and keep your current permitted to stay date valid when you re-entered the country.

But I have to go to Cambodia in order to activate my second entry Joe so I will actually be leaving Thailand

You need a re-entry permit now ONLY if you want to leave the country and return during the 30 day extension and you want to keep your 30 day extension alive.

It has nothing to do with your second entry using the visa. if you leave Thailand on the 28th day of the 30 day extension, for example, you'll lose those remaining 2 days on the extension, but it won't affect your visa if it's still valid.

If you stay in Thailand until the current 30 day extension is about to expire, go to Cambodia, return to Thailand for your second entry using the visa before it expires, there's no need for a re-entry permit.

Once you're back in Thailand you'll be given a 60 day permission to stay from the day you cross the border into Thailand and you can go to immigrations to extend that by 30 days after about a month. At some point your visa will expire, but it doesn't matter as long as you enter Thailand before it expires and after that you remain in Thailand.

Edited October 3, 201411 yr by Suradit69

Excellent. Thanks for your answer. I suspected that was the case bit wanted some clarification.