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This could be an ECM or TCU problem. Try to check your codes (search the code check on this site http://autorepair.about.com/library/faqs/bl189f.htm) to determine if there is a problem with your computer or a short. I ahd a similar problem where the S light would come on sporatically and only allow my transmission to shift between second and third. A rebuilt TCM (TCU) on eBay fixed the problem. If your speedometer doesn't work either it could be your VSS, it's about $50.

I have also heard that it can be the main relay. Does it happen after sitting in the hot sun? Or when you stop someplace for a few minutes? Does it start up after letting it sit for a bit? If so, then it definitely sounds like the main relay. It is located under the dash on the driver's side. The solder cracks in the heat and makes the connection again when it cools. So it is possible for you to fix yourself. Do a search for it on Google and you will find pictures of where to reflow the solder.

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Q: What causes the S light to flash and the car not to start when it is flashing sporatically on a 1991 Honda Accord even when the battery is disconnected?
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