Only for the API? Sounds odd unless there is something in the script you are writing that is off. Have you tried debugging your script to make sure the necessary data is being properly formatted and sent to the API? I'd check there if you cannot find the error elsewhere, and especially if the correct results come back when you manually enter in the data to Google Maps.
Like webfoo I also see some mismatches sometimes, from a few meters to a few hundred meters. But never hundreds of miles. When I use the coordinates from my GPS they hardly ever corresponds with the location in google maps. Aren't your lat/lon positions in degrees and minutes while google maps want them in degrees and decimal degrees? That could give you a large error, especially near the equator. You can also consider posting this question in the Google group for the Google maps API. There it is also allowed to post a link to your map for others to check it.