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If I am on cash accounting and the company that pays me is accrual (or not), it causes a 1099-misc issue at the end of the year. the company pays $x on December 31 and reports it on the 1099-misc. I receive the check on January 6 and deposit accordingly. My records show the income in the new tax year. 

 

Legitimately we are both correct in filing in the respective years, however if  I do, it can/will raise a flag with the IRS, correct?

 

How is this handled in TT. in years past TT would ask if the amount entered is different from 1099 box 7. I dont see that any more.