IPhone – iCloud backup from new iphone is lost when restoring old backup

When you restored your phone, did you do the configuration steps in iTunes or on the iPhone itself? Try restoring again, and follow the steps on the iPhone, not in iTunes. I've seen some reports claiming that iCloud restores can only be started from the device itself.

Not all versions of iOS can back up from backups made using more recent versions (i.e. the backups are not necessarily forwards-compatible). Confusingly, rather than show these unusable backups in some way (e.g. disabled with an error message available on tap) they simply don't show up at all (at least with iOS 5.0.1).

A new-from-the-box iPhone isn't necessarily running the latest version of iOS; it's running what was latest (or close) when it was boxed. If the version on the phone is older than the version that was used to make the backup (which is actually quite likely now that iOS updates can be done over-the-air).

Thankfully, there is a simple fix: choose to set up the phone as a new phone, rather than from a backup. Skip the step where you are asked for an Apple ID, since you won't actually be using the phone like this.

Once the initial setup is done, plug the phone in to iTunes and choose "Restore" (you can skip the backup of the clean-state phone). This will download the latest version of iOS and install that first, and then offer to restore (either from backups on the computer or iCloud).