Strange their should not be any problem upgrading. Only the default settings files are overwritten when upgrading but not if you are running in portable mode.
Verify if it really runs in portable mode. check the about box. under Menu > Help > About
In the Information box, does it says "Running in portable mode : Yes"
If it does then the settings that are loaded are the one stored in the config/ in the folder that MultiCommander.exe is started from. Then copy the backup files here.
If is says "No" then the config file under "C:\Users\<username>\AppData\Roaming\MultiCommander\Config\" ( type ":goconfig" to go there ) is loaded.
If the backup settings file are configured for portable mode then you will have "<config global="1"> in the beginning of MultiCommander.xml
then even if it says "No" in the about box you can copy the backup file over to the config/ folder where MultiCommander.exe is, and then when you start it should say "Yes"