Not everything works well, and not every example of co-operation is a shining example of cross-border harmony. The German-Polish border shows us what can go wrong and it's worth taking a closer look to try and figure out why.
History is the short answer, but more recent history than you might think. There have been cross-border co-operation programmes along the German-Polish border since the mid-nineties, but it was only with Poland joining the Union in 2004 that the programmes became fully integrated from a financial and implementation point of view. The situation was exacerbated by the fact that there were three programmes along the border, because the three German Laender refused to co-operate with each other in a single programme. Nice.
The real difficulties within the programme appear to have arisen because the German Laender have been basically able to run the programmes as they liked up to 2004. Before then, there was Structural Fund money on the German side, managed by the Laender, and pre-accession funding for the Polish side, managed by the Commission Delegation in Warsaw. Thus, it came as a nasty surprise to the Germans after 2004 when the Poles suddenly started behaving like a - shock, horror - Member State and asking difficult implementation questions and raising doubts about some of the projects the Germans wanted to fund.
Essentially, the three programmes need to operate as fully joint programmes, and, unfortunately, the impression that is given is that both sides of the border are pretty separated from each other. Much work needs to be done.