Decided to post this before I go. Wasn't sure how long it would take to do the screenshots and stuff.
This is from my Kikat Note 4 while writing using the S Pen... Note that both my Note 4's look exactly the same, with the same toolbar. Might be an update thing since I'm not updated.
This is the saved document in S Notes...
This is from my Note 10.1 2014 while writing using the S Pen...
The saved document in S Notes...
Thanks for letting me know your procedure. I did the same thing while I was testing earlier on. The thing that threw me off was your S Note's toolbar. As you can see, my Note 4 toolbar looks different. Is your toolbar fully expanded? Might be a silly question as if I deflate my toolbar, almost nothing shows... just a left arrow to expand again.
Yes it's a mystery. Have you tried clearing the S Note app cache in application manager yet? I'm not sure if you should clear data in the app though, as I don't know what will happen on certain S Notes versions. On my Note 4 and Note 10.1, if I clear both app data and cache for S Notes, it resets S Notes back to the very first time I used it. I have to go through selecting the cover, template, etc. And initially, any data I previously had will not show up. However, after a restart of S Notes, the old data does show up. I do know that S Notes stores data in Storage>Misc Files... and if you delete that data, you lose all your S Note data (don't ask how I know this!). This is how it is on my Note 4's and I assume tablet (haven't tested that). A lot of people clear the Misc Files without realizing that this is where S Notes stores the "real" data!
In any case, try clearing the S Notes app cache to see if that helps... and if you're brave enough, the app data....
BUT not before you back up your S Notes data. You can export everything to your internal memory, (and copy the backups to the SD card if you wish), for importing later if something goes wrong. This I leave up to you because I have no idea how your version of S Notes on MM works.