Background and objective: Phonocardiogram (PCG) signal analysis is a non-invasive and cost-efficient approach for diagnosing cardiovascular diseases. Existing PCG-based approaches employ signal processing and machine learning (ML) for automatic disease detection. However, machine learning techniques are known to underperform in cross-corpora arrangements. A drastic effect on disease detection performance is observed when training and testing sets come from different PCG databases with varying data acquisition settings. This study investigates the impact of data acquisition parameter variations in the PCG data across different databases and develops methods to achieve robustness against these variations. Methods: To alleviate the effect of dataset-induced variations, it employs a combination of three strategies: domain-invariant preprocessing, transfer learning, and domain-balanced variable hop fragment selection (DBVHFS). The domain-invariant preprocessing normalizes the PCG to reduce the stethoscope and environment- induced variations. The transfer learning utilizes a pre-trained model trained on diverse audio data to reduce the impact of data variability by generalizing feature representations. DBVHFS facilitates unbiased fine-tuning of the pre-trained model by balancing the training fragments across all domains, ensuring equal distribution from each class. Results: The proposed method is evaluated on six independent PhysioNet/CinC Challenge 2016 PCG databases using leave-one-dataset-out cross-validation. Results indicate that our system outperforms the existing study with a relative improvement of 5.92% in unweighted average recall and 17.71% insensitivity. Conclusions: The methods proposed in this study address variations in PCG data originating from different sources, potentially enhancing the implementation possibility of automated cardiac screening systems in real-life scenarios.