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If you have LLC with several members - it is treated as a partnership for tax purposes.
Partnership should issue schedules K-1 to each partner (and to the IRS) reporting pro-rata share of net taxable income/loss - http://www.irs.gov/pub/irs-pdf/f1065sk1.pdf - please verify which forms did you received from the LLC.
That form should be used for your individual tax preparation.
So - if LLC has an income - your share of such income is your taxable income.
If the LLS distributed part of your original contribution - that is not your taxable income.
If you overpaid your income tax - you may claim a refund, but please be aware that there is three years statute of limitation to claim a refund - starting from the date when the tax return was due.
Thus - the 2005 tax return was due on Apr 15, 2006 and the statute of limitation to claim a refund run out on Apr 15, 2009 - so you may not claim a refund for 2005.
You still may claim a refund for 2006, 2007, and 2008.
To do so - you need to file amended tax return - use the form 1040X - http://www.irs.gov/pub/irs-pdf/f1040x.pdf
File a separate form for each year and mail to the address in instructions - http://www.irs.gov/pub/irs-pdf/i1040x.pdf
Filing an amended tax return - if all information is correct will not put me under scrutiny from IRS.
Let me know if you need any help.