bilyo1.. The IP problem we will leave aside I think, this perhaps also could go in another thread too there will be plenty of others who can help you there, I would think.
2.. The use of the C-309a in my opinion has absolute no influence on the behaviour, as I mentioned you may like to go back and use this if you want to print on CD DVD media.
3.. No need to apologise for your posting, I was just hinting that the better the 'bait' looks the more likely you get a catch, in this case having showed some ppd code you caught me, I was very tempted just to leave it alone, I am starting to get a phobia over ppd internals

and I would not be surprised if
bitzbox has a good laugh reading this.
4.. If you now have got rid of the mirroring, it seems to me that the backside is either
rotated 180 degrees when it should not or it is
not rotated when it should. Just to clarify have you tried combinations of only the two, ie flip and rotate. If it does not work, I am not surprised, this is the wrong location to fix it. It is an emergency fix for an individual user but if it fixes such a problem the user is not going to complain too much (until he makes a change and forgets the patching).
5.. No the extra code you have listed I don't think has any influence on the duplex problem, but I will say I am only 95% confident because of something I read in the bug report. If it has an influence we are barking up the wrong tree here. I will ignore the code at the moment. I can later show you where this shows up and if you like to play you can customise your own web interface with your own 'signature' when dealing with CUPS scheduler (not very practical though, but looks good perhaps). I will leave this at present.
6.. Great if you have used Unix, you are a perfect
victim 
, Gnome could throw me out but I don't think so on account of the CUPS but good you mentioned it as I can run my Gnome version to check things. I can basically install any printer driver via CUPS but the last step printing is not possible this is where the
victim is needed. Presently I have 4 instances of your C-309 installed (left out any extra letters) and they only took a few minutes to install via Web Interface. I had to get the 3.10.9 but again I don't think the version plays any role, it is an insidious code piece somewhere that is a problem for Linux.
7.. I am concerned about you keep mentioning running as root. You mean you log in as root at the login process? You are not just asking for root priviliges like su (like when PCC asks for system password?) We need to look at that later but let us fix the printing problem first. Don't let me forget, though this does not have my interest like the printing.
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When using CUPS this location is very important:
/etc/cups/ppd/xxxx.ppd I am just brainwashing any readers here. In your case you have already found your "printer que configurations" don't worry about my terminology at this tage.
/etc/cups/ppd/HPPPremium309gm.ppdIn your preferred web browser in the address line:
http://localhost:631 does that bring up the CUPS management system? If so have a look around and then try to put PCC aside for the time being as we will look at printing from web CUPS and command line aspect, you can always go back to PCC.
Edit:Something vaguely stirred about Gnome. I don't think Gnome auto starts CUPS, when I checked with a liveCD it did not, so to get the correct page up I do once in root konsole:
service cups status Followed by
service cups restartMostly I just employ the last one, if
cupsd was not started a failure message will show with the restart, if it was already running I see two OK markers instead. I am sure there is a GUI equivalent but I have not chased that up because of the simplicity of using the konsole. I am sure there is a way to start CUPS when the pc is turned on.
To attack your duplex problem I will email you a HP hpijs ppd file for your printer and this should only take 30 seconds to install, I will send it if you want to go ahead, this is far easier than explaining how to get the ppd in the first place. (I did not want 40MB on my machine just to get one 20kB file

Sounds odd but the file is/does the same as the ppd file you have installed but internally coded very differently to handle the variables/parameters for the printer (this is why it may be a fix).
Well it is up to you to decide. You will be the second person only, that I know for 100% this bleeding problem was fixed by using the
hpijs.