Just further to MrTea's comments...
I have just spent 6 hours trying to flash my EPCS device... I had a smaller test project flash to it just fine, and I couldn't work out why my larger project was not taking... It had the classic "can't locate EPCS registers" error.
Then I noticed that on the working design I had both the data and instruction buses hooked up to the EPCS serial component (in SOPC), and on the larger design I just had the instruction bus hooked up... Changed it to include the databus too and it worked... woohoo... *screams in frustration and relief*