Hey Jude,
This could be many things; really I'd reccomend trying to start at some known starting point and going from there... you mention using the reference design that comes with the lancelot card -- I am not familiar with this design but does it require a sodimm module in the apex board? Is it possible to use the exact configuration (in terms of memory) that the reference design reccomends? This would be the most ideal case as it has probably been tested, and if it did not work then the reference design creator (the lancelot supplier?) might be able to diagnose the problem.
If you cannot use the exact hardware the ref design reccomends, then I would reccomend first changing the various parameters in SOPC Builder to correctly interface to *your* memory, ensure that all pins (address/data/dqm, etc.) are properly assigned, and then run some memory test code to ensure that all of it can be read/written... then the vga example code would also need to be re-built.