This is very unscientific of me but I'm playing the 1999 double episode DVD Tholian Web against the 2004 unremastered Tholian Web DVD on two computers.
The double episode DVD I have is region 1 and the later version is Region 4 which shouldn't make any difference.
The players on the different computers say that the 1999 version is 50.0 minutes while the 2004 version is 48:13.
They start off playing in stereo and then the 2004 starts going past the 1999 version. I suspect they are cutting like a half a second of some cutaway shots so that by the 4 minute mark the 2004 DVD is 4 seconds ahead of the 1999. I'm watching it carefully and eyeballing for deleted scenes. Its difficult to spot very small differences in scenes. Its only that the episodes are in slightly different places on both computers that I can tell there is a difference.
So then I would conclude that the 1999 version has more footage than the 2004 version except I found an extra 5-10 second scene at about the 40 minite mark on the 2004 version. So you can't really say that the 1999 or 2004 version is better. This scene is in the bluray as well so only missing from the 1999 version. Unless my 1999 version is faulty (its 14 years old) but it seems to be a logical unimportant scene to cut.
Is there any other explanation for the time difference that anyone can think of. I can't interchange the playback on the computers as both computers are differently region coded.
All I'm thinking is that both versions have different footage missing.
I'm going to look at the Empath when I've got time. Its the only other 1999 version I got