Hello Jim,
Thanks for your efforts.
Altering the FIFO width finds the WV5/DLL unaffected since the FPGA code pads everything to 16-bits before sending it to the cypress, i.e, it works without a problem.
Though, altering the depth as you have said works with smaller capture sizes (4K) but not with more than 8K samples which was a bit strange since the FIFO size could support it. In any case I am onto something different right now so this might not pose a problem at the moment but I might come back to this for the sake of completeness. Someone might need this later on.
Regards,
Evros