pdflatex always runs package manager

[Jack Tanner]

I'm on Windows 7 with MiKTeX 2.8 and LyX 1.6.7. I ran a MiKTeX update 
(using the admin version of MiKTeX Package Manager), and then 
reconfigured LyX. Now, every time I run pdflatex from LyX, Windows 
prompts me if I want to let MPM to make changes to my system. Very 
annoying. Worse, since there are two passes of pdflatex, I'm prompted 
twice. This wasn't happening before the MiKTeX update.

Should I try reconfiguring again? Should I reinstall MiKTeX? Should I 
ask this on the MiKTeX lists rather than here?

Thanks in advance.