One Sample, Different Methylation Values
I looked into this and if the effect is real, which it sounds like it is, it may be 5-formylcytosine.

Methylcytosine oxidizes into hydroxymethylcytosine, which reacts with bisulphite exactly like you expect (identically). Hydroxymethylcytosine further oxidizes to 5-formylcytosine, which behaves like unmodified cytosine (i,e. deaminates to form U). TET enzymes mediate this behavior in vivo but I can't find any data on spontaneous methyl group oxidation or what the kinetics might be like. This paper relies on the properties of 5-formylcytosine outlined above.

You could use this paper to test if that's true. Reduction with sodium borohydride converts 5-formylcytosine back to hydroxymethylcytosine, which reads as methylated under bisulfite sequencing.