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.
Perhaps an icon caching issue? (Clear Icon Cache might be worth a quick try.)
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: