This is an older post. But for what it's worth.
I had a similar situation... after researching a bit I came to the conclusion that the best fix was to cut the actual PCIe X1 card slot bus so that it could accept the Video card completely. The chances of messing up delicate components is far less then chopping pins off a card... but, you have the much more daunting aspect of possibly frying the whole Motherboard. Either way you are hardware hacking and it is a possibility something may just go wrong. Not to mention the chance the hardware may just not like the configuration and fry every component on you the moment the switch is thrown. I did believe this was my best option because if it worked I would be able to upgrade without any more technical issues.
In my experience it worked great. I tested with a Radeon x600 and I currently run a Radeon HD 4670 512MB GDDR3 PCIe 2.0X16 card in the X1 PCIe slot of a Dell Dimension E310 which has been modified. Works great.
In your situation I don't know if it would work anyway as you are already running a GPU in your main PCIe X16 slot. My experience with this only includes AMD cards also. Maybe that could be a factor.
I did see a thing on this guys web page here --->
http://3.14.by/en/read/videocard-pcie-conversion-x16-x1
As you can see he did it the hard way and he didn't get a good result first time through but had to do a little more tweaking to get it right. He states that his GPU needed to have pins shorted in this kind of configuration so that it knows how to act X16, X8, X4 or X1 so he tracked down the info somewhere (on the internet I'm sure)... it kills me this dude is not more specific with this post! It might be directly related to your problem though as his card was an Nvidia 8400GS as you can.
The dudes a beast. If I knew his secrets... LOL
Dude's a hardware hacker from hell!!! Check out the hot glued fan to the passive heatsink mod! This guy inspires me. LOL
Ok sorry... In my case it didn't go like that... it fit right down in the itty bitty x1 slot and just worked.
I was prepared to have it all blow up in my face.
That's just how these things go I guess. Sometimes they just work.
Maybe in this case you need to shunt a wire across a couple of pins of your card to do the magic trick this guy pulled? Maybe study the pick... because he didn't give very detailed steps with the procedure or where he found the info. It may just be the magic trick that does get everything fried for you! LOL
All I have to say is if you read this and haven''t given up yet and you still got an itch to try something else... Good Luck!