I don't know what to tell you to do to fix this, but I ran into a similar problem when I was trying to get my machine up and running for the first time. Luckily I know some good software engineers who were able to straighten it out for me. One thing you'll discover about Arduino/RAMPS is that you're going to have to recompile the firmware a lot, and the Arduino IDE is a bit flaky, like many OSS projects. You'll be hunting through 3 or 4 different config files to find the variables you need to change, then it will be time to recompile. Ugh!
When I rebuilt my printer, I switched to a
SmoothieBoard and have once never regretted it. All configuration variables are stored in a single text file on a uSD card that plugs into the board. Every time the board boots up, it reads the config.txt file. There's no hunting for the right file to modify and no recompiling. Firmware updates are applied the same way- store the new firmware binary (which you download from Github) on the uSD card and reboot the board. Done. There are about a hundred other benefits to the Smoothieboard over A/R, including much more reliable motor drivers, connections brought to the edges of the board, etc.
Ultra MegaMax Dominator 3D printer: [
drmrehorst.blogspot.com]