Elijah,
The Commissioner should issue the Letter of Good Standing if all returns up to 2011 ( period ending 28 February 2012 ) has been submitted and there are no outstanding amounts on your account. The letter should then be valid until 30 April when the 2012 return should be submitted.
With regard to the battle with registration, I think the error is on the website and you should just try from time to time. The electronic submission really simplifies matters. - Just make sure that you complete the "organisation details" tab e-mail address otherwise they will post your assessment.
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