So, I waited months before upgrading to Yosemite assuming that I would avoid the early bugs -- guess not. Somehow I forgot to test PI before switching. The first thing I found is at dragging a file over the window does not work. I understand that the reason is understood and while I did not see this said I presume some future version of PI will fix that. The more disturbing issue is this "mouse disappears" issue. I can contribute a bit of info that might be of help. I have only just played with PI a bit under Yosemite so this is a preliminary report. I am running 01.08.03.1123. The latest java sdk was installed (jdk-8u31-macosx-x64.dmg) as Yosemite seems to no longer install java and my bank needed it.
1) for some reason invoking PI from the spotlight search bar or double clicking on it's icon in the applications folder does not reliably start PI. In fact, it seems to start it every other time!!!!!! Or so I thought. In fact it looks like if you try to restart it before the app is completely closed, but after its windows are all closed then it does not restart. This is probably not a real issue. But if you left a window up until the very end of shutdown the user might not be surprised with it seeming to not restart. Since I alway auto hide my application bar it took me a few times to catch on.
2) If I double click on the background and then open a file from the file menu. The file does not appear on the workspace, but I can select it with the widget in the lower left of the bottom bar. It then becomes visible but the name tab has a blue background and the mouse cursor disappears over the image making PI unusable for many operations on the image. Cloning it generates another unusable "blue tab" image. Probably this is just some mode I'm unaware of and have not yet figured out how to toggle. Once you do that once, you seem to be screwed. Opening a file with the file open dialog box gives you the same blue labeled unusable image. You are doomed to have to shutdown PI . Now, if you wait until PI is totally shutdown and restart it and remember to NEVER drag an image over its window -- this will be very hard to remember because that is how I always use it and NEVER double click on the backgound to open a file but alway proceed from the file/open dialog from the menu bar, then it looks like you are alright. I am mystified as to why the later two paths behave differently.