Just guessing and/or thinking out loud but...

The 640x480 happens to be in the standard 4:3 ratio for TVs.

Possibly this is Media Player doing some sort of conversion on the fly so as to display the movie int he correct aspectg ratio. Possibly compensating for non-square pixels?

What do other apps think the resolution of the clip is? have you tried importing it back into Premiere and seeing what it thinks it is and/or looking at the file properties in Windows Explorer if you can get at them for MPEG2 in Windows.