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I haven't had by-pass surgery, but I did have surgery for a perforated ulcer in 1975.  It was an emergency surgery, where if my wife hadn't taken me to the ER at 4:00 AM, I wouldn't have made it.  They said I had about one hour to spare.  They did a procedure known as the Bill Roth II, where they removed about 60% of my stomach and some small intestine and sewed it all back up.  Because of the surgery, I lost about 80 pounds in the next year.

Now, I have developed chronic pain issues over the past 10 years or so and when I have been on ER medications such as Oxycontin, I never seem to get the full benefit of the med.  I have a very high tolerance and my GI tract is very fast.  I get about 50% value from the medications I take.  Although I didn't have the same by-pass surgery, mine was very much the same.  All I can say, is make sure your doctors know and if they are up on the situation they will realize you aren't getting full benefit from your medications.