I took a distribution from my Roth IRA last year and received the
resulting 1099-R.  This distribution was part of my contributions from
past years and per IRS rules, not subject to taxes or penalties. 
However, as I am preparing my taxes in Turbo Tax - there is no option
to indicate that this distribution was from my contributions.  Rather,
the program automatically adds it to my income and reduces my refund. 
The only way to bypass this is to not fill in that 1099-R information.
 The question is, since I know that distribution is not subject to tax
and if I exclude it from putting it in Turbo Tax - will that cause a
problem with the IRS (esp since IRS gets a copy of my 1099-R)? 
Thanks.

I am not 100% certain, but as a non-taxable event you should not put
it on your taxes anywhere.  If the IRS questions your decision (via an
audit which is unlikely) then you should simply have evidence to show
them that it was non-taxable.
This would be similar to withdrawing money from a ROTH after the age
of 59.5, the IRS doesn't want to know about it just do it and keep
good records so you can clearly show what you did should it ever come
in question.

Any 1099-R needs to be reported on the return.  Nearly every type of
1099 is 'matched' by the IRS.  They recieve a copy of the 1099-R from
whatever institution that holds your Roth IRA account, and you get a
copy as well.  The IRS computer will take any W-2 or 1099 with your
Social Security number on it and make sure it 'matches' what you've
reported on your return.  If you don't the IRS will automatically send
you a letter asking about the discrepancy.

I am not sure how the program you are using works, but the total Roth
distribution should end up on line 15a of form 1040, page 1.  Then
line 15b ('taxable amount') will be 0, because the Roth distribution
is not taxable (based on the facts you've presented).  There ought to
be a way in the program to put in the gross distribution and the
taxable amount seperately.  If you are still confused or having
trouble with the program, it might be worth it to see a tax
professional to avoid making a costly error.