Well - I've now installed to my other mac mini. It's doing it there too. So, as this is a different machine, with a different remote - I'm not sure of the common thread. 
The other mac mini has a fresh install. Only thing I've installed is Plex and remote buddy, to test. 
Same thing, Itunes kicks up first.

"In iTunes > Preferences > Devices 
Down the bottom, is there anything that suggests that iTunes is pair with any remotes? 
If so, forget them"

Nothing. On either.

"Try uninstalling Candleair, and disabling the remote in Plex 
Then quit and restart Plex (maybe the mac)"

OK, did this on the original, using appzapper to remove Candleair.

"Test to make sure nothing is happening 
Enable the remote again in Plex. 
Test 
Then maybe try installing Candleair again"

Yup, still does it on both machines.

"I remember Plex had issues when I used to use it where I had to forget and add the remote to get it to work. 
Out of interest, if you do not have Plex open and up press keys on the remote, does that also start iTunes?"

No. It's only when it's gone into screensaver. it makes no odds I've shut down plex or not. 
I've tried disabling sleep, but it seems in that case, it still does it after a while. 
It's like Remote Buddy can't get there in time. Once you've quit Itunes, it all works fine.

"And there are other media apps that start and stop itunes (mplayerx) that you might want to check, but if they are not running then they shouldn't interfere."

There's nothign on the 'old' mac mini I installed for testing. The new one doesn't have much, Streamtome, servetome, it did have VLC then I uninstalled, that's about it.

Hmmm.