This issue is a little trickier to explain.
With these animated screen captures please watch the VM icon in the upper right hand corner:

Expected counts per frame:
n/a 1 2 1 1 1 1
Actual counts per frame:
n/a 0 2 1 1 1 0
This may not be the exact reproduced sequence anyone else gets but it gives the general idea of the issue.
Clicking the VM icon usually makes the accurate counts appear. Both scripts are injected and running just not shown with the badge.
Using presumed f512b4e with https://github.com/violentmonkey/violentmonkey-oex/releases/tag/v1.7.0 in Opera/9.80 (X11; Linux x86_64) Presto/2.12.388 Version/12.16
Refs:
Thanks for the look.