As mentioned in MSITE-19 DoxiaFilter does not set any output encoding. In my situation this makes site:run goal pretty much useless.
Attaching a patch for trunk.
site:run ignores inputEncoding
Fixed in r795072.
Just setting the encoding of SiteRenderingContext in SiteRunMojo seems to fix this. Please test.
I see good output with version 2.1-SNAPSHOT, thanks.