The same thing happened to me. No matter how close I got to Starbase 39, I couldn't beam down. Thank god for the forums and Lieutenant_Fubar's suggestion of changing to another instance. It worked for me!
"M" (map) -> 'Change Instance' -> let it reload, then fly towards the starbase again
Yep, happened to me and a few others last night; the problem looks like is that if you have the mission to pick up and deliver Damar Kahn ot SB 39, but go there before you pick him up, it won't let you into the SB. I had to do what others have said, change instances.