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Slow set up with nRF8001 on custom board

We have recently moved to a new PCB which puts the nRF8001 on the layout instead of plugging into a nRF2741 development module. The nRF8001 connects to a TI Cortex-M4 Tiva MCU (previously a TI Cortex-M3).

Two issues have now arose. In the setup stage the RDYN line is held high for 1s after the nRF8001 sends a Command Response Event to the Setup system command (0x06). Setup completes successfully, but takes a lot longer than it did with the nRF2741 module.

The second issue is that the 16mhz clock often momentarily gets pulled low every few ms. Similar phenomenon was seen on the development kit, but the effect is now far more pronounced.

The code used on both boards is functionally the same and is adapted from the HID mouse example. I've attached an screenshot of the ACI lines for the transmission of one setup packet and response (i.e. what happens every 1s).

http://i.imgur.com/vbMa90N.png

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