Sadly xlsx charts are not yet exported to pdf. Only charts in xls files.
Exporting the xlsx charts to pdf is in our schedule for FlexCel 7, but it is a complex thing and some months away still. To give you an idea, rendering charts for xls files was the big feature in FlexCel 4, and it took about 6 months of heavy development. Now xlsx charts are in a completely different format, and I expect a similar time to make them, since there is very little we can reuse and we need to rewrite a full new chart engine.
For the moment, the only workaround is to use xls files for files with charts that you need to export.