Whoa, has this become the catchall thread ?
1. Popup Help
Sounds like this is something that came and went. I have noticed this happens occasionally too but haven't been able to work out what causes it. I have my eye on it anyway.
2. SynthMaker not fully closing
This can happen if there's a crash and the software is left waiting on a thread to return that never does. Not sure there's much that can be done about this. What we can do is look at stopping the crash in the first place so if you can find a way of replicating the crash then please do let me know and I'll look into it.
3. Locking of image files
I thought this was fixed some time ago. I dragged in an Image module and loaded up a png. I then tried editing and saving the png file and it worked fine. This was all done using 1.1.6. I'm assuming this doesn't work for you? Or are you both doing some different?
4. Slow Handling of Some Images
Are you using very high res images? SM is no Photoshop so it's not designed to cope with ultra hi res. It should be fine with images around 1600x1200. In vast majority of cases I think that they would be way smaller than that.