Scintillations are caused by ionospheric irregularities and affect the amplitude, phase, dispersion, and related parameters of GPS signals. Both L1 and L2 are affected in a somewhat uncorrelated fashion. Adequate understanding of the effects that ionospheric scintillation has on GPS signals is essential in order to produce a GPS receiver that is immune to the degradation of signal caused by these scintillation-related effects. Access to the internal workings of commercial GPS receivers is not provided to users. However, in order to understand, control, and mitigate scintillation effects, it is necessary to have access to tracking loops and associated components such as local oscillator. The software GPS receiver developed by the Center for Remote Sensing, Inc. allows the user to access its internal workings; hence facilitating advanced development of GPS receivers under different conditions. In this paper we present the results of analysis of GPS signals under scintillating conditions. Raw signals under conditions of ionospheric scintillation at Ascension Island have been processed using our software GPS receiver in order to derive the scintillation parameters. The receiver has been configured to provide stable operation during scintillation. We describe the receiver architecture, particularly the portion involving the tracking filters and related components, and demonstrate their performances under scintillating conditions. The software-based approach used by us allows receiver implementations which are suitable for ionospheric monitoring as well as for reliable operation during scintillating conditions. The improved architecture may be used for several other applications.