We can't know. You have not told us anything about which PDF settings were used, which colors/ swatches, what version of AI and Acrobat, what system and so on and ultimately what it actually looks like. For all we know you simply created the gradient in such a way that it would require to be flattened/ converted to pixels, but in the vain hopes of retaining vectors you chose not to do it in the PDF settings or something similar. Most definitely something like that....
Mylenium