hi,
what eep's are in there?
cause one time with a simple at24c01c (they have different algo, like xilinx ones, if you compare them with st and other mainline ones) me and a more experienced electronics engineer with lot of experience, took it in the face: the eep programmer read/verified OK the eep, but in fact, the eep programmer used the 'mainline' algorithm so the read/write/verify was pure garbage, but the garbage 'checked out'.
we finally nailed it out (cause the machine controlled by that eep told us we are stupid, so back to bench and correctly programm the eep)
so don't exclude a simple mistake on your eep parts on verifying side wiyh your eep programmer.
put on the table what eep/ the data you extracted and the programmer you used, maybe someone see something
in your case, the 'machine' tells you something you don't catch