if you are using the disable splash screen option / or the .ini settings file at all(i think) it will not write any newly changed settings. ie: background image, font settings etc...
i think this could also be related to plugins not working as well.... havent tested. but i remember trying to install plugins and some were not working.
ive traced my problems back to the point where i went to use the settings ini and thats when it all started. temporarily moved out the ini file and tested, program started saving settings again.
love to help a good product.
what helped for me was to edit the MirandaPortable.ini to the following:
# This INI is an example only and will not work until placed according to the directions in readme.txt
# The above options are explained in the included readme.txt
Now everythings saves as usual