This problem happens quite often. You plug in your scan tool and after a few minutes you get a message on the screen that the tool can't link to your car's network. Scan tools usually suggest you power down the tool, turn off the car's ignition and give it another shot. Typically this procedure will fix the communication problem and on your second or third try you get access to the system.
There are several network protocols in use by the automotive industry and quite often your scan tool is too fast in its protocol testing process and the car doesn't have enough time to respond back in the affirmative. By the time the car's network processes a connection request and responds, the scan tool has already moved on to try another protocol. It could be a scan tool problem and trying another brand or model may solve the issue.
Aside from the scan tool itself being the problem, there are two frequently recurring causes.
1) The battery voltage is low and isn't producing a strong enough electrical signal at the diagnostic port to establish communication with the scanner. In that case, starting the engine and retrying the connection request can boost the signal and the scan tool may be able to make a proper connection.
2) You get the dreaded "check engine" light, and when you try to hook up your scan tool you can't connect to the car's network. After many failed attempts and even with the engine running, the link to the car can't be established. In most cases this problem occurs when the fuse (either the fuse itself or the fuse wiring/socket) that's protecting the OBDII diagnostic circuit is faulty.
The problem is the when the OBDII circuit is faulty do to a fuse issue, it will trigger the "check engine" light. However, when trying to connect your scanner you get a "Link" issue and can't get into the car's computer to check for a code -- a Catch-22 scenario.
This "Catch-22" should be the clue to check the OBDII fuse and/or fuse socket for problems. Chances are a blown fuse is what set the "check engine" light and prevented the scan tool from gaining access to the car's network.
