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If ifunbox recongnize your newly Jailbroken iPhone as Jailed
Install afc2dd from Cydia after iPhone/iPad Jailbreak
please try this. 

Total Control of iPhone/iPad File System
Manage files on your iPhone or iPad in a way just like Windows File Explorer but more robust and friendly. Easily transmit files and folders to your computer with the performance optimized file transfer and browsing. File system of firmware 3.0 is now fully supported.

Hi-Speed General Purpose Storage
Use your iPhone as an USB Portable Disk for general files. Exploit the large flash memory on iPhone or iPad with transmission speed beyond 5MB/s on iPhone and 15MB/s on iPad.

General Purpose File Search on iPhone
Search files in the entire file system of iPhone/iPod Touch/iPad by matching files name and sizes. Seach files or folders can also be done within a specified folder.

Export Music and Movie on iPhone/iPod 
Export Apple iTunes© managed audio and video in iPhone, iPad or iPods to PC as a backup copy or burn to CD. Scan and populate music and movie files in iPhone and iPod even when iTunes is refused to connect.

What's New: 

Release Notes

i-FunBox New Release

Uploading Photo to Camera Roll (iOS 4+)

Fast Preview in Camera Roll (iOS 4+)

Thumbnail Preview for IPA package
Rollback to old UI style
Robust binary plist conversion