The logo image is uploaded to the "uploads" folder regardless of the default folder set in Miscellaneous Settings. Refer line 277 of register-plus.php.
1 - change line 277 to refer to your image upload folder. This is NOT my preferred solution because you are changing base code.
2 - upload the logo file in Register-Plus as normal. Then, in addition, FTP the logo file into the folder that you specified in Miscellaneous Settings. This is the preferred solution because Register-Plus can find the image and the code remains intact.
Note sure how things work with development of this plugin; perhaps the plugin developer would give some thought to issuing a patch.