This is a Known Problem and has been addressed in PSoC3 ES2 Silicon Errata. The ADC End-of-Conversion (EOC) output of the PSoC Creator component can only be used to route to one DMA channel. The EOC output cannot be used to route through the DSI routing to any other digital resources. The decimator DMA route bypasses the DSI routing avoiding this issue. The decimator interrupt integrated into the PSoC Creator component also bypasses the DSI routing. All other possible EOC connections require DSI routing.
Note: This issue has been resolved in the latest PSoC3 ES3 Silicon.
The CPU can poll the EOC bit in the status register (DEC_SR [Bit 0]) or use the decimator interrupt to signal the digital system using firmware and a control register.