I ran into this problem when trying to update my Nexus 4, first with Wug's Toolkit then manually thru ADB - it only worked when the phone's USB storage was set to PTP (Camera) mode and as the OP noted, only the Photos and DCIM were visible. Here's what I posted on XDA:
* Media Device (MTP) Mode - ADB and Toolkit say there is no device connected, regardless of whether its booted or in bootloader/recovery. Device doesn't show in Windows Explorer, so unable to move files. In Device Manager, it shows under Android Phone as Google Nexus ADB Interface, but not as a Portable Device. On the Device Stage it shows under the Unspecified area beneath the Devices and Printers and Faxes lists. It doesn't show in the AutoPlay list, though my digital camera and old Galaxy S2 (neither of which are connected) are listed. When I run "adb devices" query, I get nothing in the results.
* Camera {PTP) Mode - ADB and Toolkit see the device and work. Device shows in Windows Explorer, but I'm only able to access DCIM and Pictures folders under Internal Storage; no system folders show so unable to move files. In Device Manager, it shows under Android Phone as Google Nexus ADB Interface and under Portable Devices as Nexus 4. On the Device Stage it shows under Devices, but not in AutoPlay. When I run "
adb devices" query, I get:
List of devices attached
0xxxxxxxxxxxxxb device
I'm running Win7 Pro x64. I've tried different USB cables. I've wiped and reloaded the drivers with the Toolkit's manager. I ran SDrecan on the Nexus 4. I've Googled a lot and can't find a fix for this specific issue. I've noticed it sometimes previous Androids taking time to show up in Explorer - can't recall what i did to fix it - but this case is being a PITA.
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I haven't tried Airdroid, but ES File Explorer has a FTP server under Tools>Remote Manager which when you turn it on gives you an address (e.g.
ftp://192.168.1.24:3721/) that you enter into Windows Explorer (not a browser) and you can drag and drop files from another Explorer window.
OK, just tried AirDroid and it's pretty snazzy. Not crazy about having to register with a 3rd party to use the app compared to something like ES File Explorer or WiFi File Explorer PRO. Of course, if simply plugging in the darn cable worked, we wouldn't need all this rigmarole.