It is fairly common for pad pend and non pad pend ponies to have differences - they would have been produced in different batches at slightly different times so it is always possible that there is a genuine and not faded colour difference between the ponies...but you should note of course that with the tens of thousands [plus] of certain ponies produced in different factories, at different times, in different batches, even though HB will have put in place pantone guidelines and colour references, you may will get the occasional and minor difference in colour!
Is her whole saddle off in colour? That would be a very even fade especially as her eyes dont appear to have changed.
She is such an underrated pony so congrats on a lovely find!