Updating your g1
Keep in mind that by decreasing the percent value, you are pushing off the work to the concurrent refinement threads; hence, you will see an increase in concurrent work.G1 GC processes references during an evacuation pause and during a remark pause (a part of the multi-phased concurrent marking).
You can find part one on Info Q July 15, 2013: G1: One Garbage Collector To Rule Them All.
Both Region 1 and Region 3 happen to be referencing objects in Region 2.
Therefore, the RSet for Region 2 tracks the two references to Region 2, the "owning region".
These scan times are represented in the GC pause as "Scan RS (ms)" in the GC logs.
If the Scan RS times seem high relative to the overall GC pause time, or they appear high for your application, then please look for the text string "Did xyz coarsenings" in your GC log output when using the diagnostic option -XX: G1Summarize RSet Stats (you can also specify the reporting frequency period (in number of GCs) by setting -XX: G1Summarize RSet Stats Period=period).