Are there any settings within TortoiseGit about where / which programs the icons or shell extension appear in or how they are cached or updated? (e.g. TortoiseSVN has an option to show them nowhere, everywhere or just in Explorer.)
If they're still wrong even after a reboot then I'm not sure what is happening. Opus is not directly involved in looking up which icon or overlay to use; it asks Windows, which in turn allows shell extensions like TortoiseGit to affect the outcome.
Turning off both Preferences / Folders / Folder Display / Disable Tortoise icon overlays in the file display and Show TortoiseSVN status icons in the Status column, just above it, may also be worth a try, in case the hooks we use for TortoiseSVN are affecting TortoiseGit in some way. (AFAIK they shouldn't, but I might be wrong.)
A third thing that is also worth trying, as it fixed a similar issue for someone else: