I have been having an issue with my Galaxy Nexus. Sometimes, at random, when I get an incoming call and answer it, the call volume for the speaker will be pushed up to maximum volume.
I tend to set the volume of the speaker to have 1/2, but sometimes it just sets itself to the max and I do not know why. I don't really use the speaker phone either, so it's not the speakerphone setting.
Your correct, i just played with it. Speakerphone and regular speaker are not affected by media volume controls. They do use the same volume control, speakerphone volume affects regular ear speaker volume. Not sure why its defaulting to max though.
Did you ever get to find out what was causing this issue? I don't have nexus but I have same problem with galaxy note 2. In-call volume goes up to max randomly... And I can't seem to find any answers for this issue.