the new value is stored in the Register but has no effect!
Sorry wrong Type CY8CMBR3102!!
The changes made to the configuration registers (0x00-0x7E in the register map) take effect only after they are written to the Non Volatile Memory (Flash). Hence each time, a configuration register is changed, the CRC for the entire configuration register map has to be calculated, saved to flash and device has to be reset. This is done to avoid any abnormal behavior due to RAM corruption over a long time. Configuring MBR3 has been discussed in Section 5: Configuring CY8CMBR3xxx of the MBR3 design guide: http://www.cypress.com/?docID=50318
Hence you cannot change the duty cycle of the PWM without writing to the Flash and performing a device reset.