You should be using RCBugFix and not RC-5. The RC-x is in place just to make the starting point for the Release Candidate very clear and easy to get back to. But RCBugFix has all the improvements to the Release Candidate. And as it turns out... Your problem is already fixed in RCBugFix.

(RCBugFix got promoted to RC-5 a week or two ago. Things are much better than RC4's base.

As for EEPROM usage.... You are better off leaving that turned off until you get things up and running. Otherwise it is very easy to be fighting problems you don't need to fight. The problem is if the EEPROM is turned on, and values in the EEPROM are loaded and used and the settings in Configuration.h are ignored. You need to do a M502 (to load default Configuration.h settings) followed by a M500 (to write the current configuration to EEPROM) to get things setup every time you make a change. Its just easier to turn off the EEPROM until you have everything crossed over to the new Configuration.h file.