I've been suspicious of the order of operations in the begin() function of the RF24 driver.

Specifically these lines:

  // Reset current status
  // Notice reset and flush is the last thing we do
  write_register(NRF_STATUS,_BV(RX_DR) | _BV(TX_DS) | _BV(MAX_RT) );

  // Set up default configuration.  Callers can always change it later.
  // This channel should be universally safe and not bleed over into adjacent
  // spectrum.
  setChannel(76);

  // Flush buffers
  flush_rx();
  flush_tx();

  powerUp(); //Power up by default when begin() is called

  // Enable PTX, do not write CE high so radio will remain in standby I mode ( 130us max to transition to RX or TX instead of 1500us from powerUp )
  // PTX should use only 22uA of power
  write_register(CONFIG, ( read_register(CONFIG) ) & ~_BV(PRIM_RX) );

Theoretically, I think it may be best to reset the IRQ flags and flush the buffers after powering up and entering standby, but the failures are a bit sporadic, so I haven't been able to verify if this will reduce/prevent issues on resetting. A larger user base or additional testing may be able to prove it one way or the other, so thought it worth mentioning.