Probably because you didn't restart matchbox. The easy way is to reboot.

BTW, that's not a "strange problem" -- it's a known issue, described in the documentation. The options for matchbox window management include a fully-controlled setting, where dialogs are fixed at the center and cannot be moved, and a free-floating setting where they may be dragged around the screen. Unfortunately, the free setting causes them to be initially placed at 0,0. (There's also a version of the matchbox binary with enhanced behavior...)

In the latest version of easy-deb-chroot, this setting may be toggled (and matchbox restarted, to activate the change) from a couple of menu entries. In older versions, it's been always on, but gets reverted when uninstalling. However, manually restarting matchbox is still necessary.