This has been a huge pain, but I think I know the problem now.
First I noticed that my wallpaper was stuck, what-ever I changed it to, on start up it kept returning to one I was getting bored with. Then I noticed some fonts had changed, and again, if I increased the size, it either had no effect, or changed itself back at the next start up. It was the same with the settings in the Mint Menu, I could make the icons larger, but they would shrink the next time I started up.
It seemed worse with Chromium, some of the fonts did change on my Firefox Browser, and stranger still, AdBlock on Chromium lost all it's settings? But the thing really annoying me was the tiny fonts on the panel and menues.
Anyway, after plenty of reading and fiddling, I reloaded any things I thought may help. I was just about to give up and re-install a clean copy of Mint 13, when I notices a line under the theme I use saying font sizes are selected by the theme. I use a custom theme, just Mint-X with the X box coloured red, I think it's called 'Cherry on the Top'. Anyway, it's Mint-X causing the problems. If I select Mint-X theme some fonts, particularly those on menues and the pannel go very small, but if I pick another Theme, the fonts appear as I want them.
So I can set up my system as I like now, with large enough fonts and icons. But when I reboot it goes back to some small fonts again. I'm guessing it's either a conflict between old and new stuff on my machine, (switching between Mint-X and Mint-Z theme makes the CPU max out according to the System Monitor?). Or the settings are stuck in a config file somewhere.
Any ideas of what to try or which config files to look at? These problems seem the same if I use x-script or Mate 1.4 on start up.