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.
The region matters very much. Region 4 includes countries which use PAL, region 1 is NTSC. The native framerates of the two standards are different, PAL has a well known ~4% speedup applied to content that originated from film. Hence why your 2004 copies run time is a little bit shorter. However, nothing is cut.
50 mins (Region 1) x 4% = 2 mins, which is what you see in the Region 4 run time: ~48 mins.