I have auto save set to 9 min, however working on a project for 2 hours today didn’t produce a single .bak file and you can all guess what happened after 2 hours…
What can cause this and can anything be done about it? Turning auto save off? 
I’ve had this happen from time to time, myself. Have never figured out the conditions that brought it on. What I do know is that in my case it’s been intermittent. I also believe, though I don’t have hard evidence to back this up—it hasn’t happened for at least a couple of months— that in my case it’s been project-related.
Chewy
I would:
Toggle AutoSave off.
Exit Nuendo.
Relaunch Nuendo.
Change the time to save value and toggle AutoSave back on.
Exit Nuendo.
Relaunch Nuendo.
Load a Project, save it with an incremental name change and then monitor your .bak file progress.
Sometimes them little digits get confused and need a bit of help from the humans.
I remember Auto save being broken over 20 years ago, and people the odd time complaining about it, and I could never fully trust it.
If any plugin crashes N10.3, you may not even know about it, and the Auto may not kick in. I am so used to CTRL+S, that I never stopped doing it
every few minutes, even with Auto save at 7 minutes, and set to 3 backup files.
All that being said, in my system it is working fine.
You’re brave! 8-0
3 minutes and maximum number of .BAKs here …
I usually do the manual save ever so often but for some reason not yesterday… Think I have set it to 10 bak files.
lol. Yes but I combine with manual save every few edits.