I really don't know if this will help any... but I'll try to explain what mine has done since day one.
Sorry for the length, but I don't know of any other way to explain it. I've learned to live with it.
Here goes...
I do not use the GPS for navigation, merely a map on the dash. So, I have the navigation prompts turned off.
I do however, listen to the mp3s I have stored in it through a link to the aux port on the radio.
What I've had happen... is, while listening to the mp3s at a moderate level while stopped and the automatic volume control at speed is pretty much the same, every now and then a second Volume would kick in. Usually, much louder than the original setting... and usually while I'm stopped. I've noticed that when I turn it back down to the comfortable level the opposite happens once I'm back up to speed.
The speed volume is comfortable, but then something happens and the second volume control kicks in, and now it's too quite.
I'm sure it's the NIM getting mixed signals somehow, but there doesn't seem to be a happy medium between the two volume settings. And, while controlling the volume adjustments at the handlebar switch, the volume controls indicator is noticeably different than that of just the radio. I just have to be prepared to either turn it down quickly in the parking lot/gas station or turn it back up, once on the road again.
Your description of the Prompts not being very loud makes me think the second volume control is kicking in on you, but you won't know it unless you catch it during an actual prompt, and then attempt to turn it up at the handlebar control.
If you were able to set a navigation route with multiple turns, thus pushing multiple prompts... you might be able to catch one and adjust the volume during one of the prompts to see if it gets any louder.
Still, all in all... it's most likely a bad NIM.
Again, sorry for the long reply.