Speed using PCI Target Mode

Latency Timer configuration register is intended only for master mode. To receive the guaranteed high speed in target mode difficultly. Speed most likely does not depend from altera PCI IP. It is very strongly depends on many factors. First from a chipset of your motherboard. Secondly how you write or read data from the controller. Try to use mmx, sse, sse2 mov commands instead IA32 mov and burst reading or writing.