I might be able to help, but could you give a little more info.? Like: Are you using a jailbroken PS3? Are you using a regular PS3? What type of PS3 are you using (fat, slim, super slim)? Are you using a modded controller? Are you using a regular controller?
There might be a malfunction in your primary controller. Try this: On the backside you see a sticker with a code. Located above the upper right rounded corner of the sticker is a little hole. Get a pin (not pen) or needle and poke it in the hole. You should here a little click. This lets you know that you have successfully RESET your controller. See if it works from there...
If the problem persists, try another controller. If the other controller works, then there is something wrong with your primary controller...