and enabled IOMMU.
That's an option for virtualization, needed for things like pci-e passthrough. Shouldn't affect the number of cards recognized in any way, if anything I'd actually disable it (and it's probably disabled by default).
Am I better off returning the motherboard and getting a new one. If so, what are some good options that are compatible with my FX 6300?
If you can return it then your probably should. Although I know some people use am3 systems for mining, I personally got rid of my amd boards a long time ago intel is just better for mining rigs (mostly because it's a more power efficient platform consuming less power, and there's also plenty of boards with 7* pci-e slots and 2* m2 slots, where you can connect up to 9 gpus without any splitters). So I wasn't following the amd boards for quite a while, and can't really suggest anything. If the only purpose of this rig is cryptomining then you might just sell your fx6300 and switch to intel. Either to something on z97 (if you just have to keep that ddr3 ram), or to z270 (will need go to ddr4).
Someone had suggested the IOMMU in a forum post so I thought I'd give it a shot... Looks I may have to think about switching to Intel if I'm going to continue to have this issue. Sucks because I just bought the motherboard and processor and get everything installed over the weekend. Oh well, I didn't do my research apparently haha.
One last thing that I thought of before really calling it quits. I have one of those PCI-E splitters. Is there any reason to believe that if I unplugged 2 of the GPUs from the mobo pcie slots, plugged the splitter in and plugged those 2 GPUs into that it would work? It might seem far fetched but I'm trying to exhaust all avenues to get this thing to run with my 4 GPUs.