From what I have read, an iPod (new 30gb video) can be hooked up in two places, the head phone (mini jack) and the dock port (plug on bottom where it charges). The mini jack lets the user control the iPod entirely through the iPod, everything from the volume, to track selection, and so on. This method is alright for no audiophiles because the clarity isn't as good as the dock port. The dock port is a line-out connection, and depending on how its hooked up, allows the user the control just the track selection throught the iPod and enables them to control the volume through the HU. This is a plus because gain settings and such aren't as accurate with the mini jack (gains aren't set with the iPod, but with the HU's level out).
I have tried both, pluging the iPod to my aux input (CDA-9825) using the mini jack and the dock cable. And the bottom line is the mini jack on top SUCKS! There's no comparison.
The way I have it hooked up is I have the iPod mounted, an adapter plugged into the dock port (allows me to charge the iPod while playing), from there a mini jack to RCA cord, hooked up to a RCA to ai-net adaptor (for HU). Its pretty confusing, but sounds great. I'll dig up the thread that shows what i have going on.
Another thing, I don't know about your HU, but Alpines have an ai-net switch on the bottom of them. The manual says to switch this whenever something is pluged up, well dont! I turned it on and had the same symptons you have, no clarity, no bass, all vocals and highs. But again, I don't know if you have somehting similar on your HU.
Hope this helps somebody, if not you!
Here's that thread:
http://www.caraudio.com/forum/showthread.php?t=139642 The only thing I dont like abot it is the white adaptor and cable, that might change here soon!