A couple clarifications ...
Greg you're right about manually managing an iPod, under manual management any play history or rating changes from the iPod don't update your library. However, there was a time when the iPhone behaved differently such that plays and rating changes would register with iTunes even if you were manually managing. There is a thread somewhere around here on how this changed such that the iPhone behaves like the iPods do (either an iOS or iTunes update about a year ago changed this).
In any case, even under manual management the playcounts on the device itself should increment, that's always been the case for iPods and all other devices. If this is not happening, then perhaps an iOS and/or iTunes update changed that behavior. I refuse to manually manage, so I don't know if this is a bug or if the OP's device needs to be Reset or Restored to correct this.
The Last.Fm Scrobbler used to update like you say but now there is nothing for it to update anymore.
The plug-in for your computer or the app? Like I said, there was a new app released recently that allows live scrobbling (not an updated version of the original Last.fm app, which was lame, but a whole new Last.fm app called "Scrobbler"). I'd be curious if that will scrobble for you (there is a setting in the app to turn scrobbling on or off, so make sure its on). This new app simply serves as a front-end to your native Music app and plays the things you already have on your device, and it has it's own version of "Genius" to make a playlist of similar artists that are on your device, pretty cool.
But in any case, your iPhone should be updating playcounts on the device itself even if you're manually managing. Are you verifying this by connecting to iTunes and navigating into the contents of the iPhone? Also, what happens if you click the "Sync" button in iTunes while connected? Normally that wouldn't have an effect, but maybe that's how it works now even for manual management to register counts.
Finally, you mentioned having music on your iPhone that you no longer have access to. I highly recommend you get a 3rd party app to extract those songs -- just a matter of time that you'll have to do a Restore and you'll lose them all. In fact, it may come to Restoring to get your playcounts to update if this is not an iOS or iTunes bug.