Hi from Germany. :)
i had the same problem. after updating optiontree i was still receiving the message mentioned in the opener post. I am using mono-theme vom cudazi.
for me the following workaround fixed it. (but i am not sure, if this is really smart, because i am not a coder.)
i navigated to themes-folder > mono > libraries > theme-options.php
in theme-options.php i made the following changes:
in line 10
if ( ! is_plugin_active( 'option-tree/index.php' )
i changed "index.php" to "ot-loader.php"
if ( ! is_plugin_active( 'option-tree/ot-loader.php' )
Uploaded theme-options.php back into the folder, ... after that the message did not show up anymore.
While Derek has made some grand changes in his Plugin, the theme-author obviously couldn't notice, that Derek changed "index.php" to "ot-loader.php".
As i mentioned, i am not a coder, but this fixed my error-message-problem.
Hope this was a bit helpful? (Sorry for my bad english.) :-/