I've been running into an issue using FileTransfer on iOS that cropped up as part of my upgrade to Cordova 2.2. Previously I had been on PhoneGap 1.2 (a long time between upgrades I know). When using the 1.2 version, I could start a filetransfer upload (using sample code from here: http://docs.phonegap.com/en/2.2.0/cordova_media_capture_capture.md.html#Capture) and it would continue to run if I returned to the home screen or if I locked the device. Now it appears that suspending the app will cause a FileTransferError to occur with error code 3 and error message "The request timed out".
After trading some emails with Shazron, he pointed out that the limit to finish up background tasks is 5 seconds. If the task will take longer, the app has to request more time – and FileTransfer does not do this currently (although the CDVLocalStorage plugin in onResignActive does: https://github.com/apache/cordova-ios/blob/master/CordovaLib/Classes/CDVLocalStorage.m#L378