The solution I previously posted did not really ‘fix’ the problem. Check htaccess for the following lines:
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) yoursitename/$2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ yoursitename/$2 [L]
If your file has the ‘yoursitename’ before /$2
remove it.
The upload path issue should now be resolved in both public and admin sites.