Jeff

I have definitely had this problem when outputting from Premiere Pro CS3. Source files had already been colour corrected (not by me, I hasten to add) to 16-235 and the result after running through CS3 was a much more washed-out look.
Interestingly, Vegas uses the same MainConcept encoder.
However, if you load up a default NTSC transcode it will always try & apply a default colour profile in the transcoder. This will result in washed-out video, unless this is deliberately switched off.
I have not - as yet - been able to find a similar setting in Encore.