Gary,
3600s are "rarer" than 3100s; but, in this case, the more plentiful 3100s would be worth more than a 3600. The reasons for this are the "less desirable" features of a 3600 (as described by Highflyer).
A seller with even a little knowledge would know a Chevrolet 3600 from a 3100 - no 3100s had a "long bed". Someone changed the hood side badges with 3100 badges because they are more readily available as reproductions. If the seller is a shyster, the door plate is most likely missing.
Did you buy this from a dealer/professional or in a private sale? Did you buy the truck from a listing on Stovebolt.com?
If the truck is in nice shape and you like it, you are OK.