As Dr. Tikhonov points out, phase can change the envelope of your spectrum without shifting the peaks, to first order. A multi-mode semiconductor laser with back-reflections that alter the effective phase of the output facet as seen by each mode would be an example of a source that is actively changed. There could also be an uncontrolled Fabry-Perot cavity formed between your source and the spectrometer which could be passively changing your observed spectra due to temperature or mechanical changes. Parasitic FP cavities might be formed by poorly joined fiber couplings, reflective lens surfaces, etc. In both active and passive cases, the effect would be changes in peak heights without significant changes in peak wavelengths.