I looked into this earlier this year/last year but I can't find the post. Anyway, this is what I've worked out from reading around the web:

The G1 series has been remastered twice. The first US release was by Kid Rhino, and used pre-broadcast masters as the broadcast masters had deteriorated. The company they contracted to transfer the soundtrack to 5.1 added in a whole bunch of sound effects which were not originally present. Apparently they're very loud and sound pretty terrible. The pre-broadcast masters also used unfinished animation segments and had some animation mistakes that Rhino attempted to correct, often poorly.

The second US release was by Shout! Factory, who cleaned up the majority of the sound effects and mistakes introduced by Rhino. It's not perfect as some sections had to be restored from lower quality sources but it's a lot closer to the original.

As far as I can tell, the first Madman release is based on the Rhino release while the 2012 remaster is based on the Shout! Factory release. I own the 2012 version and haven't noticed any obvious problems.