X-ray diffraction systems based on a microfocusing X-ray source and multilayer side-by-side optics are suitable for X-ray diffraction studies in a variety of fields, such as protein crystallography, due to their compactness and low cost in maintenance. However, new problems can occur, such as intensity instability induced by source position drifting. Various investigations for the reasons and the consequences of the instability are presented in this paper. Feasible solutions and suggestions are given to obtain more stable system performance.