If in the source code there are two System.in.read instructions only the first one invokes the input box. The first character typed in the input box is correctly returned by the first read instruction, whereas the second typed character (which is the return character if a 1 character string has been typed) is returned by the second read instruction. In the attachment it can be found the source code concerning this issue.
drjava 2012-08-18-r5686 executed under winxp s.o. with java 6 (1.6.0 update 35)
Source code