I use a password manager called jpasswords because I can run it on most platforms and it can be self contained on a usb drive. Under Unity in Ubuntu 12.04, using openjdk, it runs fine, but if it get's hidden, and maybe on another workspace, Unity cannot switch back to it. It will switch to the workspace, but the GUI will not show.
This might be related to the apps behaviour. What I am referring to is that, for security, it will time out, and next time you switch to it, it will pop up a window asking for a password. I have noticed that Unity often misplaces child windows like this. I've see it in other apps, and child windows can end up in strange places after workspace switching.