I have a similar problem. I have chosen the Blissful Blog theme and in the customize page only Fonts and CSS are marked as Custom (meaning pay for it if you want it). I have changed the colour of the background picture from snowflake blue to red but the change doesn't appear on the main site. It remains snowflake blue.
If this is part of the Custom package the option shouldn't even be available for change (it should have the same orange warning as the other Custom options do).