It could be due to impurity present in your sample. Also, did you use the same sample each time or you prepared different samples for analysis each time?
First instinct is that this must be an artifact. Check your settings :) E.g. shim adjustment, check your gain etc. I guess you are seeing additional peaks... or is intensity also affected?
u can check for polymorphism, or assymetric centres. analyze mass fragmentation also. HPLC only separation.Ur compound may have other forms with same mass or may be with imputiry /reactants