It's not an uncommon problem your facing, but ultimately if you feel you've been wronged, we'd encourage you contact an investigator with the Bureau of Automotive Repairs. You may reach one by calling (800) 952-5210.
The reason we mention this situation is not uncommon is due to something called emission "readiness flags". Readiness flags (commonly known as Emission Monitors) are internal self-tests which the engine control computer performs in order to ensure all emission systems are functioning properly. The problem is, after emission repairs, a smog station regularly needs to clear the engine control computer of past faults; subsequently clearing all readiness flag data. Without the readiness data present, a vehicle can not pass the smog test. This is normal. In order to get the readiness flags to set or become complete, a vehicle must be driven through what is known as a Drive Cycle. For certain vehicles, it could take a few days of driving (around 200-300 miles) in both city and highway traffic.
posted by SmogTips Support