Taking the most common metaphorical uses:
The main metaphorical meaning of gold is of something that is of high value.
The main metaphorical meaning of silver is of something that is of high value, but not as much as what you are using gold to describe.
The main metaphorical meaning of lead is of something dull or heavy. (Though scientifically this is a tad unfair, gold is much denser).
So, butter is an extremely nice food in the morning, and is a very nice food at noon, but can be heavy and dull in the evening. (I can't say that I necessarily agree).
Another possibility though is that it uses a more obscure set of metal symbolism, that of alchemy and magical associations. Here gold and silver being linked with the sun and moon respectively associate them with key salubrious influences conducive to life (especially in balance with each other). Lead being linked with Saturn associates it with limitation, mortality and saturnine (dark, gloomy, melancholy) outlooks.
So, butter is healthy in the morning and noon, but a danger that could cause melancholy, limited health, and even death in the evening!
Edit: Considering that the earliest citation we've found was that found by StoneyB, and the source was a Paracelsian, this second possibility seems to more likely of the two.
Either way, it's saying it's great in the morning, good at midday, and bad late in the evening.
It's been used metaphorically:
Oh! how sweetly did the syren representative sing at first! How quickly it brought forth destruction, and proved a monster! Nero was pretty tolerable for five years, and this butter-print parliament was gold in the morning and lead at night.—The Loyal Satyrist; or, Hudibras in Prose. Written by an unknown Hand in the Time of the late Rebellion, but never till now published. (Printed in 1682, but five years after the start of the Interregnum would suggest written ca. 1654).