Before continuing, please update to the latest Flavours version which could have a fix for this already.
There have been some reports where OS X may have disabled the helper tool (possibly because of multiple failed attempts to install it) at the system level, causing Flavours to indefinitely prompt the user to install it. If this is the case, the approach below should fix the issue.
Please open the Terminal application, and type the command below (you will be asked for authentication):
sudo /usr/libexec/PlistBuddy -c "Delete net.interacto.flavours.helper" /private/var/db/launchd.db/com.apple.launchd/overrides.plist
You may need to restart your computer after executing the command, in order to test it with Flavours.