Привет. Не сталкивался, использую не miktex, а texlive.
На гитхабе предлагают такое решение проблемы:
"First of all, uninstall MIKTEX following the common steps and delete the folder found in C->Program Files.
After that:
Type: Win+R
Write: regedit
HKEY_CURRENT_USER-SOFTWARE-MIKTEX (delete this folder)
HKEY_LOCAL_MACHINE-SOFTWARE-MIKTEX (delete this folder)
HKEY_USERS-SOFTWARE-MIKTEX (delete this folder)
With these steps you delete all KEYS registered by the program during earlier installations and you can reinstall it."