There is a bug in the treatment of java generics. This happens with 1.4.2 as 
well as with 1.4.3 (didn't try other versions).

the following java code (test1) produces no member/function doc at all, 
while test2 does.
test3 still produces no docs, but emits a non-sensical warning at line 43:
C:/Projects/test/test.java:43: Warning: documented function `test3::Map' was 
not defined.

test3 is a stripped down version of some real world java code.
It has been stripped down as much as possible. Further stripping makes the 
warning go away!

 1  import java.util.*;
 2
 3  public class test1 {
 4    private Map<String,ArrayList<String>> hash;
 5    public void clear () {
 6      hash.clear();
 7    }
 8  }
 9
10  class test2 {
11   private Map<String,Object> hash;
12   public void clear () {
13     hash.clear();
14   }
15 }
16
17 class test3 {
18   private Map<String,ArrayList<String>> hash = new 
HashMap<String,ArrayList<String>>();
19
20   private String     tag;
21
22   public void parseFile (String fileName) throws Exception {
23     BufferedReader in = new BufferedReader(new FileReader(fileName));
24     String line;
25     while ((line = in.readLine()) != null) {
26       if (line.length() > 0 && !line.startsWith("#")) {
27         int bra = line.indexOf("<"), ket = line.indexOf(">");
28         if (bra >= 0 && ket > 0 && bra < ket) {
29           tag = line.substring(bra+1, ket);
30         }
31       }
32     }
33     in.close();
34   }
35
36   private void update (String param) {
37     ArrayList<String> list = hash.get(tag);
38     if (list == null) hash.put(tag, list = new ArrayList<String>());
39     if (param != null && param.length() > 0) list.add(param);
40   }
41
42   public boolean hasParam (String aTag) {
43     ArrayList<String> list = hash.get(aTag);
44     return (list != null && list.size() > 0);
45   }
46 }

I'll attach a zip file containing test.java, the cfg file used, a log of 
the doxygen run and three html files produced.