I have a prusa i3 and have been trying to calibrate it. I have been trying to upload the new steps per mm and I get to done uploading. However when I go into Repetier host and type M503 to get the printers settings it still shows the steps as 100 for the y axis, it needs to be 96.1810. I am using ramps 1.4 I think, with Adrunio mega 2560. If I am remembering this correctly isn't there something you have to do when uploading a new sketch like hold the rest button or something?
See here for why you shouldn't calibrate your X/Y-steps. The value of 100 is probably better and will give more accurate prints overall than the value you came up with.
When uploading new firmware you generally do not have to press any button. Pressing reset manually is only necessary when your upload method does not provide a reset pulse, but if you upload with USB this is not necessary.
What is probably causing your problem is that the E-steps are stored in EEPROM, and uploading new firmware does not override the EEPROM settings.
You should run a
M502 to restore the default settings from the firmware you uploaded, then
M500 to save them to the EEPROM.