In 2006, Bauer became the focus of news media attention over his history of speeding tickets and related driving charges, including a warning for driving more than 100 miles an hour. Bauer reportedly told the state trooper who stopped him that he was "just running late as usual." Bauer denied that he should favorable treatment due to his office. Eventually, he agreed to walk to work each day instead of driving a state vehicle.

On May 23, 2006, Bauer was injured in a single-engine airplane crash that occurred shortly after takeoff from a small airfield in Blacksburg, South Carolina. Bauer was the pilot of the Mooney M20E propeller-driven aircraft. He and his co-pilot escaped the wreckage with minor injuries before the plane caught fire. A National Transportation Safety Board (NTSB) investigation found that the crash may have been due to pilot error. The NTSB report concluded that Bauer should have aborted his flight, noting that his plane had insufficient speed for takeoff. Bauer later sued three companies that had worked on the plane's engine, alleging negligence. One of the defendants was fined for improper maintenance of the aircraft.

As South Carolina’s lieutenant governor, Bauer earned $46,545 annually. However, he was also paid for his role as president of the S.C. Senate. Over a two-and-a-half-year period from Jan. 1, 2008, through June 30, 2010, Bauer was paid a total of $27,650 as the Senate president, Senate records show. Combined with his salary as lieutenant governor, Bauer earned at least $144,000 during the period, according to an Oct. 12, 2010, report in The Nerve.

Of Bauer's total Senate compensation, $22,925, or 83 percent, was “subsistence” payments, according to Senate records. That money was for lawmakers who lived outside of the capital city, to reimburse them for their hotel and meal expenses while the legislature was in session, The Nerve reported.

When asked about his subsistence expenses and other Senate payments in a September 27, 2010, phone interview, Bauer told The Nerve that he lived in Greenville County. The investigative website reported that according to Richland County records, Bauer had owned a condominium in downtown Columbia since May 2008. That residence was located less than a half mile from the statehouse. Bauer did not seek re-election as lieutenant governor and said he was selling the condo.

While running for governor in January 2010, Bauer compared helping poor people to feeding stray animals at a campaign event.

Lt. Governor Bauer's position at the Office on Aging was largely ceremonial, though he did exercise executive authority over some administrative decisions. He appointed Curtis M. Loftis, Jr. as the Director of the Office on Aging and approved the office's budget. In 2012, the Lexington County Recreation & Aging Commission honored Bauer by naming its senior center in Batesburg-Leesville after him.