I blew up the the waveforms of all 3 LD releases (90, 93 box set, 98):
http://img.photobucket.com/albums/v420/trailerparkboy/98LDinvertedwaveform_zps660fbba9.png
As you can see, the 98 waveform is inverted compared with 90 and 93.
You'll have to compare the scenes on the 90 or 93 LD while, say, viewing the same scenes from any DVD/BD on your computer and you'll clearly notice that the scenes are cut. For instance, before the dialogue begins during the dining scene, some of the shots during the back and forth close-ups of Stephens and AE are missing. Similarly, during the opening scene some of the back and forth shots between Al Mulock and the pair of bounty hunters approaching the tavern from the opposite end of town are missing.