The guy who runs komugi.net let me know this had been fixed. It only affected ROMs being compiled for the last 2 weeks in October. All November nightlies should be OK. CM 6.1 rc1 IS NOT OK and should not be used if you are a Docomo customer unless you edit the apns-conf.xml file prior to flashing.
The fix was provided by Takuo Kitame, who is responsible for the Japanese translations in CM, who had this to say when he fixed the error on October 29th (short and sweet):
APN: change order of 44010.This timing was too late for me because I'd already been charged by then. Ironically it is the same day I flashed back to the safe TMUS CM6 remix. Unfortunately for Apiddo and any others who will pay an extra 4200 yen in November, the word didn't seem to get circulated in English. Maybe I need to start following these guys on twitter (even though I don't want to use twitter). All subsequent nightly builds will have the correct order and shouldn't be a problem for us.
"mopera.net" should be below the "mpr2.bizho.net" because it's too expensive.
The take home message is to be careful with APNs and consider yourself lucky that your carrier doesn't charge you the full packet rate for these types of snafus.
And one final thought: I still don't understand what the purpose of having mopera.net included.