01 Honda Civic Immobilizer Trouble

I just completed the install of my alarm/starter in my '01 Honda Civic SI. The alarm/start is an Autostart brand. I also installed a DEI 555I immobilizer bypass. Everything appears to be working fine, except for the following nuance. If the vehicle is started with the key, the immobilizer light on the dash continues to flash (signaling that a valid key has not been inserted). The car will start fine and run, but the light on the dash will continue to blink. If the vehicle is started with the remote start and the key inserted and ignition enabled, the light on the dash does not blink. Has anyone seen this before? Any ideas what is causing this. As a mention, during the install I did not hook up the factory disarm wire. Not sure if this is related in anyway. Thanks,

Are you sure the YELLOW and the YELLOW / Black are NOT reversed??MO

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I am pretty sure that everything is hooked up correctly. After I posted the message I did a search through the forum and found a couple others that were having similar problems. The solutions that were offered were to use a relay to bypass the module when the key is inserted. I don't know if this is the only solution. I would rather try to understand the problem and search for an alternate resolution before trying the relay bypass. When I have a spare minute I am going to check all the connections, but I thought I would see if anybody has had a similar problem that they resolved. Thanks for the reply.