Old employer distributed 401K by check, reported box 12a then I deposited into new individual IRA. Report as contribution? Report as repayment?

No. You should have received a 1099-R; the IRS will also have received a copy of this 1099-R. You will need to report this 1099-R rollover distribution on your tax return but none of it will be taxable. 

Just make sure that when you are reporting this information into TurboTax that for the question "What Did You Do With The Money From (your retirement fund)?", answer "I moved the money to another retirement account (or returned it to the same retirement account)" (See the attached screenshot below. Click to enlarge.)

Please feel free to post any additional details or questions in the comment section.