This happens due to a software bug in PD 5.0 when writing the commands to flash. Please ensure that the device revision for CapSense Express devices is 1B and download the PSoC Designer 5.0 SP6 from the link http://www.cypress.com/?rID=34517 which fixes this bug.
The device revision can be read using the following command from the Bridge Control Panel Utility:
w 00 a0 00 r 00 x p
The reply expected from the device is:
w 00+ A0+ 00+ r 00+ 1B+ p
Note: You'll have to reorder the samples, if the device revision is not 1B.