No idea why it's doing that... but you can change it manually...
Go to your game directory - for Steam it is as follows:
"Steam\steamapps\common\eufloria\Resources"
and find the file "user.settings"
Look for the PLAYERCOLOUR setting, and make it 0, which is the red/blue colour scheme.
(also, check to see what it's set to now in case it's something weird)
Then see if it lets you change it.