First please program valid RCW on your custom board, QCVS DDRv tool doesn't have JTAG configuration file overriding RCW function.
If there is SPD on your target board, please create QCVS DDR project with "read from SPD" method. If no SPD, please create the project with default configuration, then modify Properties panel according to DDR data sheet.
Please capture low level CCS log to me to do more investigation.
When you connect QCVS DDR project to the target board, the CCS console will pop up at the right bottom of the Windows task bar.
Please open CCS log and type "log v", then connect to the target board again, the low level CCS log will be printed out. Please capture this log to me to do more investigation.