siterates vs partitioned per site analysis

[idaios]

Hi!
I play with a small dataset, trying to follow the manual of MrBayes. Thus, I have just 2 sites, I used a fixed tree, fixed branch lengths. My goal is just to infer the per site evolution rate.
Thus, first I used the report siterates=yes, but the results look totally nonsense. Actually, I have a site nearly monomorphic (with just one missing value) but the reported rate is huge.
Second, I used the partitioning scheme:
charset pos1 = 1;
charset pos2 = 2;
partition bypos = 2:pos1,pos2;
set partition = bypos;
prset ratepr=variable;

now, it reports both a m{1} and an r(1) result. And I cannot understand what they do mean and what is their difference...

best
pavlos