"R" stands for "Refresh", meaning it's shipped with support for new Xeon 5600 series processors. If you're using a non-refresh board, you'll have to update BIOS to 45 or later before you can use a Xeon 5600 series processor.
I just got a S5520SC and I was planing to use a Xeon 5600 series.
I don't want to buy a 5500 just to update the bios.
Can I use a flash programmer to update the bios using the cap file? Or is it not recommended?
One of the main reasons why the refresh boards were launched was because it was easier to identify which board comes with the bios version 45. All refresh boards will have bios 45 installed.
Here is a link which can answer some of your questions:
All the best,