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William H. Berry was elected in 1906, shortly after the dedication, to the office of State Treasurer on a reform "fusion ticket". Berry was the only Democrat elected to a statewide office from 1895 to 1934. His successful campaign was deemed by Governor Pennypacker to be "one of those freaks of ill fortune". Berry began investigating the costs of the capitol project and brought its $13 million pricetag to the attention of the public. Part of the reason for the discrepancy was Pennsylvania's "over-elaborate" and sometimes "unintelligible" method of "ordering and purchasing supplies, equipment [and] furnishings, commonly called the 'per-foot rule' ". Because the methods of measuring under the "per-foot rule" were not rigorously enforced, furnishing could be, intentionally, overpriced by the supplier. For example, a flagpole installed on the capitol roof was priced at $850; Berry estimated the value of the pole to have been only $150. Other expenses included $1,619 for a $125 bootblack stand and $3,257 for a $325 "mahogany case in the Senate barber shop".Pennypacker tried to demonstrate that costs associated with the capitol were reasonable in comparison with similar notable structures.  He pointed out that the United States Capitol cost $18 million, but had "fifty-five less [rooms] than the Capitol at Harrisburg." Pennypacker also showed how the New York State Capitol had cost $24 million, and was still unfinished. After an investigation, a total of five people, including Huston, were convicted, on December 18, 1908, and sentenced to two years in prison for "conspiring with State officials to defraud the State in the erection and furnishing of the Capitol." The Superintendent of Public Ground and Buildings James Shumaker and Auditor General William P. Snyder were also convicted. Among the convicted, John H. Sanderson and William L. Mathues died before going to prison.

conspiring with State officials to defraud the State