This study concerns the task of automatic structural heart abnormality risk detection from digital phonocardiogram (PCG) signals aiming at pediatric heart disease screening applications. Recently, various systems based on convolutional neural networks trained on time-frequency representations of segmental PCG frames have been presented that outperform systems using hand-crafted features. This study focuses on the segmentation and time-frequency representation components of the CNN-based designs. We consider the most commonly used features (MFCC and Mel-Spectrogram) used in state-of-the-art systems and a time-frequency representation influenced by domain-knowledge, namely sub-band envelopes as an alternative feature. Via tests carried on two high quality databases with a large set of possible settings, we show that sub-band envelopes are preferable to the most commonly used features and period synchronous windowing is preferable over asynchronous windowing.