I had a similar problem with my 2007 TBA at around 250 miles on odometer. Several times she would not shift up to 3rd. Sometimes It was real annoying since I was in traffic. However, I have not noticed it since then. I always wondered if it was something due to that first real ride I took (put on ~180 miles that day). Since then, the 600 mile service has been done and I have not experienced that problem again.
Conwy

Blue/White 2007 TBA, Thruxton needles, Unifilter, AI removed, Polaris Bellmouth, Bubs, Nology Coils/wires, Lightbar, Ricor Intiminators, Hagon Nitros, Tall Sissy Bar w/luggage rack, Dart flyscreen & Lowers. 130 Mains, TrueGel Battery MG12-BS.