The thing about 5.5 vs 6.0 is a possibility. Also, it is my understanding that on windows it is typical to create a .bat file, but obviously this would not be the case on Ubuntu...but is there perhaps some configuration file?
There is no need to create a .bat file either, it's just a shortcut for convenience of the user not to enter the same parameters again and again (and a .sh file would do the same for Ubuntu)
And no: ccminer does not use external config file - neither windows, nor ubuntu version. There is NO sign of such in the source.