The word is featured here not because it is in itself odd, but because of the way that its modern sense of something firmly fixed or established has come about.
One of the most ancient dyestuffs is a deep red colour that today we call crimson. The Greeks got it from a scale insect that lives on a type of oak tree found around parts of the Mediterranean. Some Roman writers, such as Pliny, referred to the insects as granum, grain. There is some excuse for this, since the way the insects cluster together makes them look like a clump of grain.
Following this Latin usage, in Medieval English people spoke of engraining something or dying in grain for dyeing cloth with it. But over time, people began to think the word really referred to the grain of the cloth, like the grain of wood, and that the word meant, not dying with a particular colour, but dying it to its very roots, colouring it throughout its whole substance.
The adjective engrained, originally describing something dyed crimson, slowly altered its sense to refer to a person whose characteristics were so firmly fixed as to be unalterable. Over time, the word changed its spelling to ingrained.