A PEM fuel cell stack is usually integrated with a reformer into a stationary fuel cell power system. Reformate may cause a phenomenon of voltage vibration in some cells of a stack, and these cells are usually close to end plates. In this work, we studied the instability phenomenon within a 10-cell stack. The instability was observed by monitoring the voltage variation of each cell at high currents. From the test of the assembly pressure distribution, it was found that the pressure distribution of cells close to the end plates was more uneven than others. The scanning electron microscopy (SEM) was used to observe the microstructure of gas diffusion layers within these cells. These scanning electron microscopy images showed that the gas diffusion layers close to end plates suffered more fibers damage, i.e. disabling the hydrophobic structure. The contact angle test results supported this concept as well. In this study, we interpreted that the instability was caused by flooding. If a stack clamping apparatus, providing uniform compression, was used to clamp the stack during testing, the performance of each cell remained stable even in harsh operational conditions. In this paper, it is considered that the pressure distribution of gas diffusion layers is intensely related with water removal ability as reformate is fuel for a proton exchange membrane fuel cell stack.