I can confirm erratic mark disappearances. Usually they seem to persist through several bouts of closing and opening Leo, but I'm never sure they will be there.
BTW, I have set up these hot keys for marks:
F4 - go to next mark
F9 - set mark on node
F10 - clear all marks
I used these keys because they are used in EditPlus, and I have many years of habits from using it. The only difference is that in EditPlus F9 toggles a mark rather than simply turning it on, and I like that behavior better.
@ekr, would you be amenable to adding a mark-toggle command? If so I'll post an enhancement request on GitHub. I imagine it would be pretty easy, so I could probably adapt existing mark and clear code myself, come to that.