That is already set. So it might be the ROM?
If you set the second option, or one similar, have an active data connection, and the applications still will not update, it can very well be due to the ROM.
However, I have seen some picky applications that refuse to update over Data, possibly due to it being unreliable, as it is 3G, or that the application requires a strong connection to the internet, through a Wi-Fi, due to whatever requirements the developer insists on.
I would, if the ROM has one, go to its thread and mention this issue. I have not heard of Google applications or options being tampered when flashing custom ROMs, but I have heard of issues with 4G, Google Maps, Google GPS, Google Navigation, and for some odd reason, MMS, when flashing almost ANY kind of ROM. If the ROM has specific read mes or follow ups, it might be worth to read up and bring yourself up to speed, in the event the issue is already known and a solution, permanent or not, has been found.
I am surprised, you are running this phone on 3G? Is 4G not available? How did you even manage to get it to run on 3G? *I am sorry for these questions*