I am debugging my program with apache mina 2.0.2. The specific library is irrelevant.
The problem is that Eclipse can see internal structure of some classes and cannot see one of the others. No apparent differences visible for me: both classes have both code and source.

You can see that Eclipse draws arrow near AbstractPollingConnector class and does not so near AbstractPollingProcessor.
Of course Eclipse can’t set line breakpoints inside “bad” classes.
What is the reason of it and what to do?
I guess, it depends whether the referenced classes were compiled with the debugger options on or off. According an older Javac manual, the -g switch seems related: