Yep, I’m also experiencing this problem.
ACF PRO Version 5.1.3
WP 4.0
A wysiwyg field in a flexible content field row looses the formatting after ordering the rows.
Seems to be back after a fix in ACF 4.3.0:
WYSIWYG field: Fixed JS bug where formatting is removed when drag/drop it's repeater row
Fix would be awesome!