This is actually a fairly common problem, but sadly, there is no simple fix. I had hoped with Windows 7, current chipsets and modern BIOSes, multi-monitor support would be more refined, but sadly, it is not - ESPECIALLY when integrated graphics and graphics cards are used together to support 3 or more monitors.
The only simple and consistently reliable solution I have found is to use two cards (preferably like cards) and disabling integrated. The downside, of course, is this solution normally requires a beefier PSU, the 2nd GPU with its additional fan generates more noise, and the 2nd GPU creates more heat in need of exhausting. However, the result is a stable graphics solution.
That said, even the latest operating systems sometimes have little issues, and seem to get confused occasionally as to which monitor is primary and which is secondary. So a multi-monitor utility is almost a necessity. My favorite is
UltraMon – not free, but worth it. Others have suggested the free
DisplayFusion, but I have no experience with it.
With Ultramon, there should be no need to mess with BIOS settings. In fact, I never mess with those, instead, just leave it set to "Auto".
I don't understand why all three monitors don't work together when choosing PCI.
PCI? Do understand that in spite there similar names, PCI is a totally different and incompatible interface from PCIe (PCI Express). You should not be using PCI.