I have the card set up in the slot that the manuals says (slot 4). The expansion slot utility say that is it running below max speed 4x instead of 8x but that is the way the manual pictures it. It seems to be running okay but my system will not restart. It goes to black and then nothing no start up sound. But if I shut it down and wait a minute or so it boots up just fine.
At first I thought it was the SATA card and/or drives but system restart fine with them after I pull the Kona 3 out.
I have 3.4 driver loaded. no conflicts when I run aja's utility software.
I had a very similiar problem. My Mac (an 8-core Mac Pro with 16 GB RAM and the FX 4500 card) has an LHe card. It was running the previous version of the Kona software and I was having no problems.
However, after I installed the 3.4 software, the Mac wouldn't restart. It would start up ok from being off but if I tried to restart, it only reboot partially. The screens black and I'd hear a clicking sound coming from the monitors I've got on the breakout box. Completely uninstalled the Kona software didn't help, nor did zapping the p-ram.