This isn't an APN problem, it is a SIM problem.
Your provider has one set of numbers on your card, and another set of numbers that actually identify the network, and they don't match. Technically, from the phone's point of view, you *are* roaming, even if it is the same provider. From the provider's point of view, you *aren't* roaming.
Up until cupcake, we had that same problem here in Canada when using the "Fido" network (which is owned and operated by "Rogers"). The network identified itself as "Rogers", the SIM cards identify themselves as "Fido", the phone think's its roaming.
So; you don't need to worry about roaming charges when you are actually connected to the correct network.
BUT; You don't have an easy to read display to tell you when you are *really* roaming, nor can you make configurations that are based on whether you are or are not roaming.
Edit: You might be inclined to report it as a bug against AOSP. Even though it technically isn't a bug, the workaround for it needs to be input and that needs to originate as a bug report. http://source.android.com/report-bugs