I posted something similar in one of the other threads about inaccuracies on the Nike+ site. My experience is slightly different - I've run three 5K workouts so far, the first one in 26:16, which WAS recorded on the Nike+ site as my best, the second one slightly slower, and then the third one, after calibration and the third one, thanks to calibration and extra effort, in 23:23. However the Nike+ site refuses to accept this final run as my best 5K. If I pull up the run details, it DOES know that it was a 5K run, and offers to compare it to my "best" run, which it still thinks is 26:16.
I contacted Nike too - twice, in fact, as I followed up to confirm that my iPod does store the best time correctly (under History / Personal Bests) - and, as usually happens when you contact support lines, got two slightly different responses. One saying that everything is fixed now (and no, it isn't - the time is still wrong.. unless they mean it will be fixed going forward, in which case I'll have to wait until I run again tomorrow), and the other one, an hour later, apologizing for the inconvenience, assuring me my problem has been reported to the Nike+ web team, and suggesting I check back next week...
So now, it's not just you having the problem, but I do feel reassured that Nike is working hard to smooth out these initial issues with the site.
15" PB 1.67GHz, 2GB RAM Mac OS X (10.4.7)