The computer will lower your score for checking a box related to checkride repeats, failures, 709, etc.

Some employers may be suspicious that there may have been under-handed dealings on the part of the applicant as well as the DPE (was this guy known as Santa-for-the-right-price?). Rather than do the research and try to make a judgement, they might simply move on to the next applicant. Their objective is not to be fair, but to hire people with the minimum effort and expense on their part. That's why squeeky-clean is so popular with airline HR ladies... no in-depth research or risky judgement calls required. Hopefully most will weigh this appropriately and not hold it against the applicant.