It could be a number of things. I had a stent put into my circumflex nearly four years ago and a recent angiogram showed it's still perfect. My cardiologist removed as much of the plaque as possible before ballooning the stent into the artery, because he said it will prevent problems in the future. Just squeezing a lot of plaque behind a stent, into an artery lining will inhibit normal lining growth, and scar tissue will be the likely result or more plaque.
Another reason could be the choice of stent. I believe certain brands of drug eluting stents tend to be much more prone to restenosis than others. The idea of your stent and medication is to inhibit scar tissue growth, and allow a new lining to grow. Nothing in the body will remove the hard plaque behind the stent, so new healthy tissue growth will be very difficult.
Angioplasty has come a long way since 1991, so have they even considered opening your native vessel, rather than keep attempting to clear the bypass graft?