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The remotes will not have an effect on this system. They key and the remote have nothing to do with each other. For the SKIM system you should have a gray key. The key has a chip built into the gray portion of the key. The SKIM module learns the keys code using a factory DRBIII scanner and entering the 4 digit security code. You may have a problem with the key itself or there may be a system fault in the SKIM system. I checked and didnt find any related service bulletins through Jeep for this concern. The only way to check this system is to go to your local jeep dealer and allow them to check the SKIM system for any codes then go from there. They have the means of getting the 4 digit security code. Otherwise there isnt anything else you will be able to check with out the factory equipment. Let me know if you need further help or have more questions.
Here is more information from the manufacture:
The Sentry Key Immobilizer System (SKIS) is standard factory-installed equipment for this model. The SKIS is designed to provide passive protection against unauthorized vehicle use by preventing the engine from operating without a valid key. Following are some general descriptions of the features and components of the SKIS.
The SKIS includes the following components:
Certain functions and features of the SKIS rely upon resources shared with other electronic modules in the vehicle over the Programmable Communications Interface (PCI) data bus network. The PCI data bus network allows the sharing of sensor information. This helps to reduce wire harness complexity, internal controller hardware, and component sensor current loads. At the same time, this system provides increased reliability, enhanced diagnostics, and allows the addition of many new feature capabilities. For diagnosis of these electronic modules or of the PCI data bus network, the use of a DRBIII® scan tool and the proper Diagnostic Procedures manual are recommended.
The other electronic modules that may affect SKIS operation are as follows:
Refer to Fuel/Ignition System in the Contents of Group 8W - Wiring Diagrams for complete circuit diagrams. Following are general descriptions of the features and major components of the SKIS.
The SKIS uses a Radio Frequency (RF) transceiver and electronically coded Sentry Key transponders to verify that a valid key is inserted in the ignition switch lock cylinder. If the SKIS recognizes the key as valid, it sends messages to the PCM that will allow the engine to run. If the SKIS does not recognize a valid key, the engine will not run. While the engine starting system will operate and the engine may initially start and run up to about 800 revolutions-per-minute on residual fuel pressure, the vehicle cannot be driven without a valid Sentry Key transponder.
The SKIS includes two valid Sentry Key transponders from the factory. If the customer wishes, additional non-coded blank Sentry Keys are available. These blank keys can be cut to match a valid ignition key, but the engine will not run unless the key transponder is also programmed to the vehicle. The SKIS will recognize no more than eight valid Sentry Key transponders at any one time.
The SKIS performs a self-test each time the ignition switch is turned to the On position, and will store Diagnostic Trouble Codes (DTCs) if a system malfunction is detected. The SKIS can be diagnosed, and any stored DTC can be retrieved using a DRBIII® scan tool as described in the proper Diagnostic Procedures manual.
See the owner's manual in the vehicle glove box for more information on the use and operation of the SKIS