iTunes is no tag editor. To my observation, iTunes started a couple of versions ago to not write modfications into the files but only into its own database.
So, it could very well be that you have the correct data in iTunes but it never arrived in the files. That might be that what you see in Mp3tag and other programs.
As for the comment: iTunes needs a COMMENT field being set for English. Not all programs write the COMMENT field like that but keep the language of the local PC.
Mp3tag does this also by default, but you can change that within the language file - see this thread for this problem: iTunes doesn't read comment tag when Mp3tag language is Spanish
You should check the settings for Mp3tag for what versions of tags you read, write and delete.
See File>Options>Tags>Mpeg for that.
Read & write: V1, V2
Delete: V1, V2, APE.
With the rest of your problems: it looks a lot like a combination of numerous negative influences. Yet, MP3tag will help you to get a clean collection.