In the Presbyterian Church (U.S.A.) all giving is voluntary, and the gifts are received gratefully. But a number of factors can interfere with raising the full amount of per capita that the governing bodies need. The news story cited above discusses some of those factors.
The Constitution of the Presbyterian Church (U.S.A) says in G-9.0404d.:
Each governing body above the session shall prepare a budget annually for its operating expenses, including administrative personnel, and may fund it with a per capita apportionment among the particular churches within its bounds. The presbyteries shall be responsible for raising their own per capita funds, and for raising and timely transmission of per capita funds to their respective synods and to the General Assembly. The presbyteries may direct per capita apportionments to the sessions of the churches within their bounds.Note that although the apportionment is among the particular churches, the presbyteries have the constitutional duty to raise the per capita. And there is the rub.
In the Presbyterian Church (U.S.A.) all giving is voluntary. The presbyteries do not compel, and have no authority to compel, the session of a particular church to send in every last cent of the per capita due from that church (see the decision of the General Assembly Permanent Judicial Commission in Minihan et al. v. the Presbytery of Scioto Valley).
When congregations do not send in their full per capita, whether because of a lack of funds or an intentional choice, the presbyteries are caught between a rock and a hard place. On the one hand they have a constitutional provision that creates a duty to the higher governing bodies, and on the other hand they depend on cooperation from the local churches to be able to fullfill that duty.
Some commentators (here or here) have attributed the shortfall to intentional withholding of per capita by local churches. Based on my experience in the PCUSA I would suggest that most of the shortfall is likely due to financial problems in churches.
There was a report on past due per capita at the most recent meeting of Pittsburgh Presbytery. According to that report, only one congregation with a past due amount through 2005 is withholding GA per capita, and only one is witholding the presbytery portion of per capita. According to the news story one of the two synods where the withholding phenomenon is concentrated is the Synod of the Trinity, of which Pittsburgh Presbytery is a part.
The fact is that sometimes a congregation gets to the end of the year able to pay most of its bills but falls short on being able to send in the full amount of per capita. Presbyteries routinely are patient with churches in such situations, and often the congregations are able to solve the problem within the early part of the new year. When the congregations do not do so, the problem accumulates, affecting funding decisions in subsequent years.