Hello,
I often hear and use "(It's)funny how" to mean "It's strange that" not to mean "funny" as in amusing. I think it is frequently neutral or negative in this usage. Frequently the subject -verb (It is) is just dropped and understood. "Funny how" is similar to saying "That's funny." when you hear unusual or unexpected news.
EX: "(It's) funny how he always disappears when there is work to do." Means I am suspicious about why he leaves.
EX: "Funny how I hate coffee, but I love coffee ice cream." Means I think this is a little unusual or without explanation
EX: You say "John just left me a message in Spanish." I say "That's funny...he told me he didn't speak Spanish."
Hope those help a bit!
Martha