There won't be an audit because the format of the 1099b has negatives and your entries into the software don't. Audits don't work that way. They are looking for the total loss, which to report correctly per the Schedule D instructions which is what you are sending to the IRS, they should not be negative on this form.
https://www.irs.gov/instructions/i1040sd
Brokers were given the same information as TurboTax - somewhere there needs to be an adjustment so that they can be reported as they should be and a few made the changes, but it seems most did not.
When importing the software just takes like fields to like fields - it can't convert them for you, unfortunately.
This is definitely an IRS mandate - but it's in the eFile instructions given to eFile providers not anything that is easily shareable.
