Issue with textarea editor

I’m fairly certain that is the WP editor doing that and not OptionTree.

Only OptionTree metabox WYSIWYG editor have this issue

I’ll look into it for 2.5.2, though in the future please post your bug reports to the OptionTree Github repo where you will get more eyes on the issue. I don’t keep track of the bugs in this forum.

https://github.com/valendesigns/option-tree/issues

Do you have wpautop turned off for the main editor in your theme?

In order for the behavior you want you will need to filter ot_wpautop for your textarea option types.

To turn it on globally you will need to do:
add_filter( 'ot_wpautop', '__return_true' );

To add it on a per option basis you will need to do:

add_filter( 'ot_wpautop', 'custom_ot_wpautop', 10, 2 );
function custom_ot_wpautop( $value, $id ) {
  if ( $id == 'your-option-id' ) {
    $value = true;
  }
  return $value;
}