I'm using Sozi Version 20.05.09-1589035558 in MacOS High Sierra (10.13.4 (17E199)) and this "Clip" button has been turning itself on for me too (but for only my first frame; I haven't seen this with other frames), with the same surprising reframing choice (but the reframing seems to always be the same; just not the one I set up).
My process is basically:
1. Create my SVG using Inkscape,
2. Use the Sozi application to set up all frames to my satisfaction (I've been using 10 frames thus far),
3. Use Sozi to save the presentation,
4. Open the presentation using Firefox,
5. Run through all frames in presentation (sometimes using -presenter.sozi.html to launch the .sozi.html presentation, other times just opening the *.sozi.html presentation directly from the Finder.app or just creating a new window or tab in Firefox and entering the file:///path-to-sozi.html),
6. I notice some minor thing I want to change while going through the presentation in Firefox, so I close the Firefox tab/windows,
7. I open the Sozi presentation again, choose the SVG file that the presentation is based on, and SURPRISE, the first frame is now different than it was the last time I looked at it (both in Firefox and Sozi. And I find that for the first frame, the "Clip" button is blue (on) now, whereas before, it was gray (off).
I've seen this happen at least 5 times in the span of maybe 1-2 hours of working on it. The automatically selected reframing choice has eliminated one of my 3 layers as created in the SVG. I'm not using layers in Sozi though. My timeline in Sozi has only the Default layer.
To recover from this strange event, I delete the first frame, create another first frame, arrange it as originally desired, save, and repeat. Then I repeat the numbered process above, and the automatic reframing of the first frame seems to happen consistently.
I'm thinking this may be a bug? I'm trying to work around it now by making two nearly identical start frames to see what happens after I go through the same numbered process above with two identical (except for frame ID) start frames.
This little quirk is a little annoying, but in spite of it, I really like Sozi. Thank you for making and sharing it.