Strong equatorial scintillation is often characterized by simultaneous fast phase changes and deep amplitude fading. The combined effect poses a challenge for GNSS receiver carrier tracking performance. One of the consequences of the strong scintillation is increased navigation message data bit decoding error. Understanding the rate of the data bit decoding error under equatorial scintillation is essential for high accuracy and high integrity applications. We present the statistical relationship between the data bit decoding error occurrences and the intensity of amplitude scintillation based on the processing of intermediate frequency GPS scintillation data collected on Ascension Island in March 2013. A third-order phase lock loop (PLL) is implemented to process the data and to access the data bit error typically expected in conventional receivers. A Kalman filter-based PLL is also used to process the same data to demonstrate that the data bit decoding error can be reduced through advanced carrier tracking designs.