Just had a quick check and Brondby, who were seeded in last seasons 1st qualifying round, were away 2nd.
Might have been for a city clash, mind, but I cba checking more.
UEFA Cup rules PDF also states ties are determined by draw and mentions nowhere about the seeded team away first.
Meh, checked a few more:
Djurgårdens IF (seeded) were away 2nd while Man City (also seeded) were away first.