Have you tested all your PCB's with the same PC?
The Bootloader device is the default state of the kit, without any firmware which can be programmed either to RAM, or EEPROM or FLASH.
The BootProgrammer Device is like any other firmware and when you select the I2C EEPROM option on Program menu in the control centre, the control center application firstly loads the CyBootProgrammer.img present in the C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.3\bin
This BootProgrammer image can then be used to program the EEPROM or FLASH that is on board and writes the firmware image that you want to store in them.
The reasons for BootProgrammer device not coming up can be either related to the driver, incorrectly, binding to the BootProgrammer device or it can be because of some issue with the board.
Since you mentioned that only 5 out of 30 boards are failing, can you please try un-binding the driver in the device menu for the BootProgrammer device and then re-binding it to the device again?
Do the following to bind the driver manually:
1. Right-click the device and select Update Driver Software. Choose Browse my computer for driver software.
2. Browse to the location <Install Directory>\Cypress\EZ-USB FX3 SDK\1.3\driver\bin. The default install directory is C:\Program Files for 32-bit Windows and C:\Program Files (x86) for 64-bit Windows.
3. Select a driver based on your Windows version and click Next. For example, the driver for 64-bit Windows 7 is located at C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.3\driver\bin\
Also, can you please try programming the boards on a different host PC as well?
This will help understand if this is an issue with the host PC or the if it the issue with those PCB's alone.