Please read the comments in the code in order, the question details are there.
Why is this difference happening?
Please quote the JLS if possible.
import java.util.*;
/**
 * Suppose I have a generic class
 * @param <T> with a type argument.
 */
class Generic<T> {
    // Apart from using T normally,
    T paramMethod() { return null; }
    // the class' interface also contains Generic Java Collections
    // which are not using T, but unrelated types.
    List<Integer> unrelatedMethod() { return null; }
}
@SuppressWarnings("unused")
public class Test {
    // If I use the class properly (with qualified type arguments)
    void properUsage() {
        Generic<String> g = new Generic<String>();
        // everything works fine.
        String s = g.paramMethod();
        List<Integer> pos = g.unrelatedMethod();
        // OK error: incompatible types: List<String> := List<Integer>
        List<String> thisShouldErrorCompile = g.unrelatedMethod();
    }
    // But when I use the raw type, *ALL* the generics support is gone, even the Collections'.
    void rawUsage() {
        // Using Generic<?> as the type turns fixes the warnings below.
        Generic g = new Generic();
        // OK error: incompatible types: String := Object
        String s = g.paramMethod();
        // WTF warning: unchecked conversion: List<Integer> := raw List
        List<Integer> pos = g.unrelatedMethod();
        // WTF warning: unchecked conversion: List<String> := raw List
        List<String> thisShouldErrorCompile = g.unrelatedMethod();
    }
}
Side note
I originally found this in IntelliJ IDEA, but I guess that compiler is compatible with javac because when I compiled the above code with the following it gave the same errors/warnings.
$ javac -version
javac 1.7.0_05
$ javac Test.java -Xlint:unchecked
...
$ javac Test.java -Xlint:unchecked -source 1.5 -target 1.5
...
 
     
    