For the taxes I owe I wrote out a check to the Internal Revenue Service instead of the US Department of Treasury is that going to be a problem?

More than likely, your payment will be processed properly

Checks and money orders made payable to "IRS" or left blank must be over stamped with "United States Treasury" (by the IRS)

The IRS will not send the check back to you to have it made out to "United States Treasury." They want their money.