I've moved the edits here as an answer:
The theme problem
Thanks to @trashgod I've tried the following line:
ChartFactory.setChartTheme(StandardChartTheme.createJFreeTheme());
If I use this line before creating charts in my application, reports no longer affect the appearance of them. I think it is enough to put this line just once after report creation.
So now I just have one problem: the first report is different from subsequent reports: charts are different, fonts are bolder and not antialiased...
The Problem of the second report
The pdf issue is not caused by jasper reports nor jfreechart. It is a problem of Adobe Reader. This happens when you have more than one instance of Adobe Reader running (for example, when you have two different files opened).
An example of the problem:
Similar issues: