Multi-channel audio alignment is a key requirement in bioacoustic monitoring, spatial audio systems, and acoustic localization. However, existing methods often struggle to address nonlinear clock drift and lack mechanisms for quantifying uncertainty. Traditional methods like Cross-correlation and Dynamic Time Warping assume simple drift patterns and provide no reliability measures. Meanwhile, recent deep learning models typically treat alignment as a binary classification task, overlooking inter-channel dependencies and uncertainty estimation. We introduce a method that combines cross-attention mechanisms with confidence-weighted scoring to improve multi-channel audio synchronization. We extend BEATs encoders with cross-attention layers to model temporal relationships between channels. We also develop a confidence-weighted scoring function that uses the full prediction distribution instead of binary thresholding. Our method achieved first place in the BioDCASE 2025 Task 1 challenge with 0.30 MSE average across test datasets, compared to 0.58 for the deep learning baseline. On individual datasets, we achieved 0.14 MSE on ARU data (77% reduction) and 0.45 MSE on zebra finch data (18% reduction). The framework supports probabilistic temporal alignment, moving beyond point estimates. While validated in a bioacoustic context, the approach is applicable to a broader range of multi-channel audio tasks where alignment confidence is critical. Code available on: https://github.com/Ragib-Amin-Nihal/BEATsCA