Hey - if you never figured out the problem (Do you have vista?)
I remember having that issue EVERY patch, and vista is annoying.
If you haven't, try downloading the station launcher, beta I think? It's on the SOE site. Umm other than that I usually do a Google on "EQ patch not working" and people usually have some ideas :)
Just restarting might help too =P
If you don't have Vista... oh well =D you're lucky.
GL though.