What did you mean by "both"?
One is the plug in block list and the other is the malware list
"So my guess would have to be that your 2013-003 wasn't properly installed the first time."
I think it was a security or Java Update in April for me, I was stuck at May 1 until the June security update and then I got a date of May 16 and that is where I had been stuck at till last night
My thought was maybe trying to reapply the patch might get it fixed right (I know some updates get rerelased (things fixed in an update))
Same Aug 29 here on 10.6.8.
Ignore the date, just go by the version number. Yours is up-to-date with version 65.
got an error from the server that says "[...] Ignoring new signature plist: Not an increase in version". At this point, I'm updating manually once every3-4 weeks, and hoping for the best.
That's not really an error, it's exactly what you should see every day. You shouldn't need to manually update unless you hear about an update and 24 hours have passed without your seeing it.