Make sure it is enabled under Tools > Options > Portable/Audio Devices.

iphone.dll plugin enabled

But MediaMonkey sees it only when it is plugged via USB

Phone is listed in usb devices list, so it is successfully plugged.

I have the same problem: Itunes see iphone, but MM can't see him anywhere

You need the latest 4.0.5 beta

I install 4.0.5 build 1492 but this don't solve the problem. What else you can advise?
Itunes 10.6.1.7 and QTime 7.7.2 installed on my windows 7 x64