Actually, I have used only "why" for years---not sure when or why (or how come) I started doing that. Why is used in writing, and, and I write more than I talk.
More efficient output wise to type 7 letters than 3 perhaps.
Edit: For example, I should have used a lot of quotation marks or italics above---but it just seemed overkill for such a simple answer.
When I was a youth I used "how come" a lot. However, after many years of scholarly grooming and refinement on proper etiquette, I became a man of distinguishment and erudition. Now when I have the desire to comprehend the rationale of a quandry, I say with great distinction and clarity ... "how come?" (some things just shouldn't be messed with)