Joshieboi,
I am not sure whether a high data usage put them into alarm. Anyhow, it worked for five months without problem. And comparing my bills for the last months, the data usage was not so different then before.
On the APN-question. I just don't know. My iphone was activated in Thailand with my Japanese non-iphone-Sim card. So I guess it just use the APN given by the SIM card? I have no opportunity to see the APN as it is not a jailbroken phone. At least I don't know how. If there is a way, please let me know.
I still wonder what might have changed in june. Could it be that a network reset or a complete reset changed something so that Softbank was able to recognize my iphone as such? But I am not sure whether I did anything like that. I remember that I had trouble after trying out the application Find!Tokyo that blocked my iphone completely but I don't remember what I did to restart.
iPhone has different official partner throughout the world. There is something called "carrier bundle" that allows each carrier to localized its iPhone for their domestic market needs. When you input a say, Softbank SIM, iPhone will loaded up Softbank's carrier bundle and its settings. carrier bundle can have wide range of setting tweaks, things like allow editing APN settings, enable MMS, record greeting message for visual voice mail, Tethering... the list goes on and on. There is a way to modify your carrier bundle without jailbreak your iPhone. However, to do so you need to have some commend line knowledge, other wise it can really mess up all your iPhone settings.
From your post there are two possible out comes.
1. When you insert your Japanese non-iPhone SIM, iPhone just use SIM card's APN setting for internet. (There might be a way to help you out)
2. When you insert your Japanese non-iPhone SIM, iPhone recognized it as Softbank SIM, and load the preset APN setting in your iPhone.
If what happened was situation #1, then here is what I think happened.
Probably, in recent month's there are more and more Softbank's customer in similar situation as you are. In order for Softbank to prevent customer from using lots of internet access resources, they can setup computers to flag accounts with regular cell contract but high level of internet usage. Once the computer flag your account, they can have people to take a look in details. Things like the type of cell phone you purchase along with your SIM card, and type of internet price plane can quickly lead them to know if you are using a regular Japanese cell phone or Smart Phone. (Smart Phone has better web browser that allow you to view PC base web link, which can occur tons of internet packet.)
Here is my recommendation, if what happened was situation #1, then you can try to call Softbank and enroll yourself in one of the internet access plan for their X-series phones (Softbank's Smartphone line up). If they wouldn't let you, try to tell them that you purchased a used handset from Yahoo auction and the previous owner purchased it from Softbank. If everything all goes well, you should end up with your non-iPhone SIM, and a new data plan that does not flag your account with high internet usage. (Because until now, I still don't think Softbank can tell wether you are using a iPhone or other smart Phone base your internet data usage.)
All of this was just my speculation, try it at your own risk.
If what happened was situation #2, then you are out of luck. Because Softbank have different sets of APN setting for iPhone and their other non-iPhone handsets. Softbank will know which set of APN setting your phone use to access their internet service. With this, they will know exactly if you are using a iPhone from over sea or not.
** Softbank does not sell their iPhone specific SIM card without an iPhone. so if you still want to use your own iPhone with Softbank, you might want to look into this**
Go to Softbank, upgrade your account to a new iPhone 3G contract, sell the handset on Yahoo auction, keep your owned SIM card with your current SIM free iPhone.

(There are lots of iPhone 3G at very heavy discount currently, you look around)