Videos and photos take up a large amount of space. I was under the initial impression those wouldn't count.
Photos in the Photostream don't count, but those also don't stay more then 30 days in the cloud. The Camera Roll (if you aren't using Photo Stream) is backed up and counts. Photos synced via iPhoto aren't backed up.
Videos and Music synced via iTunes also aren't backed up. If you are using third party programs, they might have their content flagged to be backed up. Easiest way to check is to go to Settings - iCloud - Storage & Backup - Manage Storage - (Device Name). It should break out each app and the backup size, along with toggle switches to disable some apps. Sounds like you may have found this already, helpful for others though to know about.
Wifi sync is supposed to be on-power only. However, if you unplug power from the iPhone after it shows up in iTunes, you can continue to sync for some undetermined amount of time.
You can initiate a manual sync even when the device isn't plugged into power, and same for backups. iOS will only automatically try and start a sync, or backup on it's own when it's plugged into power. Not sure why the device disappears for you though, mine remain visible in iTunes as long as they are on the home network.
YMMV of course with the jailbreaks.
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