I'm, not sure about PC PSUs, but many of the high end PSUs that I've worked on did indeed have a sense line. Virtually no current would flow down the sense line, it would simply be used to feed the voltage at the board back into the PSUs feedback circuit. This allowed the PSU to regulate the out voltage at the consumer rather than its own output terminals, and therefore compensate for any voltage drop across the supply cable. Even if PSUs do have sense lines, that wouldn't necessarily mean that you have to wire it back with the same pinouts. If your VGA card also has a sense line inside it (and I have no idea if they do), then you'd need to wire them up the with the correct pinpouts. However, if all the +12V and 0V pins on the connectors of the video card are soldered to gether on the back of the connector, then it wouldn't matter which way you put them in, so long as you didn't swap a +12V lead with a 0V lead.
Having said all that, I'm not sure if this is even the case with your PSU or any PC PSU (But I imagine it would be, otherwise you'd introduce an unstable element via the cable voltage drop) . I had a look online for a schematic for your PSU, but couldn't find one. You could find out for yourself if you've got a multimeter with a sensative enough DC range and something to load the PSU with. Connect up the all the +12V lead to a load resistor (a powerful 12V lamp would be good for this), then measure the voltage drop across each of the wires. If you find one with much less voltage than the rest, then that's the sense lead.
If, after reading all that, you're sitting the scratching your head trying to work out what language I'm speaking in, then you should probably just wire the leads the way you found them, and be done with it.
🙂Hope that helps.
Motherboard: RIVE (3602 bios)
CPU: Intel 3930K @4646MHz
OS Drive: 2 X Samsung 840 PRO (Raid 0)
Storage Drive: 2 X 1.5TB WD Caviar Black RAID 0, 2 X 3TB WD Caviar Red, Kingston V100 256GB SSD
Memory: 64GB G.SKILL Ripjaws Z (F3-12800CL10Q2-64GBZL)
GPU: Gigabyte GeForce GTX580 @795MHz - 1536MB GDDR5
PSU: OCZ ZX1250
Cooling: Phantek PH-TC14PE
OS: Windows 7 Ultimate x64. (EUFI)