[a bit off topic]The Disc # tag wasn't. Neither were the Replaygain tags. I can guarantee you that. Nor will a tag show up if it's in the file and you create a library field to support it, i.e. a LABEL tag for the recording company name. You have to fill the tag in MC and have it write the tag again. Other than those exceptions, I will admit that most FLAC tags do show up regardless of the tagging program used.
Actually, the FLAC plugin is currently the only decoder plugin that allows reading any tag from the file so that the tag header in the file tag and inside the library are literally identical.
Your disc number tag didn't show up inside MC because the used tag headers can be different in different programs. It is possible to create a custom tag and import a different disc number tag. Inside MC you can copy the field value to MC's predefined field or you can use an external program for that (e.g.
Mp3tag).
J. Rriver developed its replay gain analysis and tagging system over six years ago (MJ was the first player with such a system). MC writes the values in its own style. Some other programs have later adopted a bit different system, which is not compatible with MC. There is no simple way for transferring the different replay gain values between these different systems. However, these two different replay gain tag sets can co-exist in the physical file tags without problems.
[/a bit off topic]In general, I would recommend using the secure ripping mode with rip logging. This thread has some useful tips and it is very much related to the topic:
Topic: How can I ensure quality of a ripped music file