The arduino runs at the following baud rates:
9600 for firmware updates (I think, not sure)
57600 for 5D firmware (stock)
115200 for Marlin/Sprinter (build3 in repG works best)
250000 for Marlin V1+ (does not work with repG 26)
Just check if you have the correct baud rates. Do NOT alter the baud rate in the system settings.
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Daid 306
Yes. It's possible to update the Arduino code. There is a firmware upgrade option in the RepG menu (even works if you cannot connect properly)
Another possibility would be SkeinPyPy-Beta4:
https://github.com/daid/Cura/downloads
This will upgrade your firmware to Marlin V1 (which is a lot newer then what's shipped with RepG) on 250000 baud. The disadvantage is that it won't work with RepG anymore then (because RepG cannot handle 250000), but the good thing is that you don't need RepG with SkeinPyPy.
The fan rotating slowly, and later fast if you turn the machine on is normal. If the slow rotating fan bothers you, you can remove the "ARDN_PWR" header from the board. It's intended use is to power the Arduino from the mains power. However, a side-effect is that the USB powers then FAN then when the power is off.
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