There has been some issues with the power adapter used for programming on the CY3649. A couple things that can be checked:- Voltage setting on the adapter, and check if it outputs 9V DC with 1A current (center negative). If these settings are correct and the programmer still doesn't work right, please check using another power adapter.
Also, the socket adapters that are used with the programmers were designed for Pb devices (Leaded devices). Although, using these with the Pb-Free parts shouldn't cause any issues, some parts may require a Pb-Free adapter due to potential electrical and/or mechanical contact issues. Attached is the link to BP Microsystems (one of our leading 3rd party programmers) Pb-Free device adapter issues -> BP'>http://www.bpmicro.com/Web/helpandsupport.nsf/WebKeys/BPM-67VMQF?openDocument&Cat=Issue">BP Microsystems Pb-Free socket adapters
The above should be checked for after making sure the preliminary steps (like choosing the right adapter, placement, matirx cards etc) are take care of.