Even if you meet the substantial presence test, you can still be treated as a nonresident alien if you:

* Are present in the United States for less than 183 days during the year
* Maintain a tax home in a foreign country during the year (Refer to Chapter 28 of Publication 17 for a discussion of the tax home concept), and
* Have a closer connection during the year to one foreign country in which you have a tax home than to the United States (unless you have a closer connection to two foreign countries, discussed next). For determining whether you have a closer connection to a foreign country, your tax home must also be in existence for the entire current year, and must be located in the same foreign country for which you are claiming to have a closer connection

So if I claimed my Australian tax return in July 2008 and did not commence working in the US until September. Although I was physically present in the US for more than the 183 days (on VWP and E-3). Do I file as a non-resident or a resident?

If you entered the U.S. in 2008 and have spent more than 183 days in 2008 in the U.S. you are dual status.