When you get a bunch of stations, clump them into one day. The reason mistakes keep happening is that I rush to update things as soon as possibe before I get behind.
It is easier to update my SLC site because I don't DX every day, and when I do, I usually only have to spend a few minutes. (I'm also not KANG about my maps being 100% accurate).
However, if I was in your situation I would probably be dxing every night with all of the new finds, but then again I have absolute power over updates so hea.
Just glob them into one big organized pile and I'll add them when I get the chance. As far as the maps, be patient, AceFTP is a crappy program and takes a while to update stuff.