Mother board is Gigabyte GA-990FXA-UD5. A 4.3.5 kernel works fine. 
Attached is my dmesg after failing to boot and going to rescue mode. 
amd_iommu_dump was set on the cmdline. kernel is x86_64

My kernel config as relates to the IOMMU:
grep -i iommu .config
# CONFIG_GART_IOMMU is not set
# CONFIG_CALGARY_IOMMU is not set
CONFIG_IOMMU_HELPER=y
CONFIG_VFIO_IOMMU_TYPE1=m
CONFIG_IOMMU_API=y
CONFIG_IOMMU_SUPPORT=y
# Generic IOMMU Pagetable Support
CONFIG_IOMMU_IOVA=y
CONFIG_AMD_IOMMU=y
# CONFIG_AMD_IOMMU_STATS is not set
CONFIG_AMD_IOMMU_V2=m
CONFIG_INTEL_IOMMU=y
CONFIG_INTEL_IOMMU_SVM=y
CONFIG_INTEL_IOMMU_DEFAULT_ON=y
CONFIG_INTEL_IOMMU_FLOPPY_WA=y
# CONFIG_IOMMU_STRESS is not set

Regards
Mark