Eclipse not picking up includes

I am trying to port the UDP example to the DE2-115 in Quartus 13.0. Currently stuck trying to work out why Eclipse isn't finding the .h and .c files.

I have successfully compiled the project in Quartus, then from the menu in Quartus, I open "Nios II build tools for Eclipse". Create a new project etc.

I'm having problems compiling because it can't locate files such as "triple_speed_ethernet_regs.h". Some files ARE getting copied into myProject_bsp/drivers and myProject_bsp/HAL. But my custom IP includes wasn't getting copied (there were only a few of these so for now I copied them into the directories manually. I can't face going through all the altera folders copying these across. So anyone know where something could have gone wrong to stop this working?

If I put the folder /altera/ip as an include it still doesn't pick them up. So something must be trying to copy the triple_speed_ethernet_regs file into the project folder?

Any ideas?