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I experienced the same problem and wrote a small patch to
solve the problem. It seems to work without problems :)

--- xmms-shell-0.99.3/src/window.cc 2002-10-23 02:05:19
+0200
+++ xmms-shell-new/src/window.cc 2003-12-22 18:01:51
+0100
@@ -58,7 +58,7 @@
status |= apply;
break;
case 2:
- status ^= ~(status & ~apply)
| apply;
+ status ^= apply;
break;
}