The first reference I can find for the seperate sprint classification is from the year 2000.
See Wikipedia's article (in Italian) on this subject: Tour de Suisse 2000.
There were 2 different sprint classifications, but I can't tell which was the purpose of that. In 2001 there were even 3 different sprint-classifications. My bet is that it has also to do with Sponsorships, like the colours of the jersey's.
