First, Mr. Barroso had to endure a three-week delay before he could take office. That was because the European Parliament threatened to veto his team of commissioners if he did not remove a conservative Italian nominee who legislators criticized for calling homosexuality a sin.
After persuading Italy to replace its man on the commission and making a couple of other changes, Mr. Barroso's team finally gained the parliament's approval last week.
But then, another firestorm developed over the French commissioner, Jacques Barrot, who failed to inform Mr. Barroso and the parliament that he had been convicted of illegally funding his political party four years ago.
Mr. Barrot was given a suspended eight-month jail sentence at the time. But under a presidential amnesty, his conviction was later struck from the books.
In an interview with several European newspapers, Mr. Barroso said that the Barrot affair has now been resolved. The French commissioner, an ally of President Jacques Chirac, was given unexpected support by the parliament's socialist group, which led the charge against Mr. Barroso's first commission.
Although some British and Scandinavian legislators continued to call for Mr. Barrot's resignation, most of their continental European colleagues say it is time to let the commission get down to business.
Mr. Barroso, in a speech in the Belgian town of Bruges on Tuesday, did just that, laying out his priorities for his five-year term. He says his main goal is the revitalization of Europe's sluggish economy. He pledged to step up research funding to help Europe catch up with the United States in high-technology industries, and he called on EU countries to devote more money to higher education.
But he also said that the strict EU rules regarding member states' budget deficits should be applied more flexibly in times of slow economic growth. That is good news for Germany, whose deficit has surpassed the limit of three percent of gross domestic product for three straight years.
Mr. Barroso and the Germans disagree on another issue, however. He wants to increase the EU budget, whereas Germany and other big contributors want to freeze payments at one-percent of gross domestic product.