No release of this film has ever been perfect on disc (note also that this film has only ever been release legitimately on DVD and Bluray in Japan; any other disc version you have seen is a bootleg).
Before continuing, a few historical notes on this film.
The movie is a 2 hour version of the original 36 episode tv series. After the series had wrapped up in 1982-1983, it was decided to do a film version for release in 1984.
In 1987, an OVA call Macross Flashback 2012 was produced. It was a mix of old and new footage. The beginning of it was new animation set to about 90 seconds of the song "An Angel's Paints". The last 3 minutes are also new footage and set to the rest of this song. The middle part of the OVA is a mix of TV series footage (originally animated on 16mm film) and movie footage (originally animated on 35mm film). The whole OVA was mastered on video (ie not film) at 29,97 fps. The original film elements for the new footage is considered lost and only the video master remains.
During the 90's, the film was released on laser disc with some of the original footage of Flashback 2012 inserted at the end of the movie and called Macross Do You Remember Love Perfect Edition.
In 2000, it was released for the first time on DVD. The version was the same as the Perfect Edition. Curiously, it was encoded rather bizarrely. It was encoded at 29,97 fps interlaced, but the disc was also progressively authored. The viewing result on an HDTV was a mess if you used a table top DVD player. At the time, only a PS2 could play it well.
In 2008, it was released again, this time in a 3 disc edition, as djmasturbeat said. Disc 2 was the original theatrical version without the flashback 2012 footage. This was not remastered and the video is grainy. Disc 3 is bonus content. Finally, disc one was our promised “HD Remastered” version. This version was the same as the perfect edition, except it was encoded at 24 fps progressive. The video was considered quite grainy for a remastered version. Also, there are 2 video glitches. During the climax, as Bodoza’s ship begins to self-destruct, for a split second, you see footage from earlier in the film. A similar glitch also occurs later in the film, except the interval is shorter (I’ve never noticed this second glitch myself). The glitches are part of the master used for the dvd.
Finally, the bluray, as is already known, has a much better picture, but is edited/censored in a couple of scenes. Also, some footage is considered slightly more blurry than others. Often one cut will be sharp, the next blurry, the next again sharp, all during the same scene sequence. This seems to be part of the original 35mm film and how they filmed it. There is no workaround for this. Also, the flashback 2012 footage used on disc 1, also looks softer since it comes from video. Disc 2 is the "theatrical version", but it also contains the edited/censored scenes. Disc 3 is bonus content, including Flashback 2012 upscaled to 1080p.
Like I said, this film has had an interesting release in Japan.