Curiously enough that is the feature and it IS documented:

"Inconsistent information. If fields conflict, the calendar will give
preference to fields set more recently. For example, when determining
the day, the calendar will look for one of the following combinations of
fields. The most recent combination, as determined by the most recently
set single field, will be used.

[...]

For the time of day:

 HOUR_OF_DAY
 AM_PM + HOUR

"
see
 http://java.sun.com/j2se/1.4.2/docs/api/java/util/Calendar.html

So in your case it didn't come up with AM_PM and the HOUR _combination_
as having been set, so it used the old HOUR_OF_DAY. The solution is to
change HOUR when you change AM_PM which could include getting the
existing value, thus the following code results in
the value you expected:

        Calendar c = Calendar.getInstance();
        c.set(Calendar.HOUR, c.get(Calendar.HOUR));
        c.set(Calendar.AM_PM, Calendar.AM);
        System.out.println(c.get(Calendar.AM_PM));

-Paul