Historically J. RIver has used their own replay gain tagging style. MJ was the first player program with internal replay gain support.
The recent MJ12 builds can read the TXXX REPLAYGAIN_TRACK_GAIN and TXXX REPLAYGAIN_TRACK_PEAK values if they exists ID3v2 tags (i.e. in MP3 files). The analyzer will automatically skip these files and analyze only the files that don't have these tags.
Read and write support for these two "TXXX" ID3v2/MP3 tags was added only recently. The goal was to make these tags compatible with the Rockbox firmware and some player devices that support this tag style.
MJ12 will automatically and dynamically create the album specific replay gain values that are used internally (there is no need to write the album gain values to the tags).
You didn't say what file formats you use, but as far as I know you can safely run JRiver's analyzer and have the MJ12 and foobar tags in the files at the same time. At least FLAC, APE, MPC, OGG and WMA work without problems.