Network Coordinate (NC) systems provide a lightweight and useful way for scalable Internet distance prediction while serving as an important component in many Peer-to-Peer applications. Most of the existing NC systems utilize the Euclidean distance model, which is largely impaired by the persistent occurrence of Triangle Inequality Violation (TIV) in the Internet. Recently, matrix factorization (MF) based NC systems, which can completely remove the TIV constraint, provide an alternative approach towards better prediction accuracy. Phoenix, an NC system based on the MF model, well explores the advantage of the MF model and becomes the most accurate NC system so far. However, through experimental study, we find that the prediction accuracy of Phoenix for short links is significantly worse compared with the overall prediction accuracy. Based on the observation, we propose a new NC system, named Pancake, aiming at reducing the high prediction error for short links. By introducing a two-level architecture, Pancake achieves much higher prediction accuracy than other selected existing NC systems. Through extensive experiments, we demonstrate that Pancake reduces the 90th percentile relative error by up to 25.37% from Phoenix. Moreover, Pancake converges very fast and is robust to different dimension values. For further insights, we study the performance of Pancake using a dynamic data set in addition to the widely used aggregate data sets. With varying RTTs over time, Pancake outperforms other NC systems consistently.