The latest release has just been approved for the Mac App Store, so it should start showing up soon as an available update.
This release contains some more fiddling with title parsing, and some other improvements specifically targeted to the making and delivery of presentations.
See the Knowledge Base for all the details.
Presentation mode is terrific. It’s a really useful application of Notenik.
I appreciate the caveat that you’ve included in the presentation pack. You’re centering the user expectations in the place that Notenik excels.
Caveat: Notenik is best used for simple, straightforward presentations that are primarily text-based.
You must know that we’ll all be sending in enhancement requests, like, “please make Notenik into a slide viewer.” 
Question:
Can presentation mode interfere with the behaviour of other collections that are open at the time?
After entering presentation mode in one collection, I’ve noticed that the check mark in the Collections > Display > submenu is not displayed for other collections that use a different display mode. Other collections in presentation mode do display the check mark.
I’ve also noticed that presentation mode can disable the edit button. I haven’t been able to identify the specifics yet. All I know so far is, when a collection is in presentation mode the edit button may not work. At first I thought this was a sensible default. Then I noticed that I couldn’t edit another collection that was not in presentation mode. I restarted Notenik to clear the memory and found that the edit button worked for the collection in presentation mode, and other collections. Then, after a certain amount of clicking and toggling presention mode, it didn’t.
Glad you appreciate the presentation mode!
Let me look into the issues you’re reporting. Right now they don’t make any sense to me, but that doesn’t mean they’re not happening.
Let me try to recreate…
I haven’t been able to replicate any of the issues you’ve reported.
That doesn’t mean I don’t believe they’re happening, just not sure what to do about them.
Curious whether anyone else is seeing anything like this…?
Also curious whether you have any spectacularly large collections you’re working with…?
I couldn’t find a definite set of steps to make it occur and the coincidence with presentation mode could have coincidence. It may be that the problem is on my machine, or in front of my machine 
If I see it happening again I’ll try to isolate the cause more closely
The open collections weren’t large. Two were about 100 notes. The two others had only a dozen notes.