Have you read this thread?
Take a look at the video and read through it, see if it matches your issue.
Adobe did release a Flash CC update specifically trying to fix this issue. Also make sure what you have your brush settings configured to isn't to straighten lines. As Flash turns your lines into shapes, internally it has to decide if you meant a very slight curve or a straight line. If the curve is too slight, it will be converted to a straight line.
We have addressed several issues related to Wacom drawing in the latest Flash CC 2014 release (188.8.131.52)
This release also features
* New and improved Motion Editor
* SVG export
* WebGL for animation
* Variable Width Tool
* Tweening for variable-width strokes
* Export as Projector
* HTML5 extension support
and much more...
To know more about what's new and exciting in Flash CC 2014, please visit
Flash CC 2014 Overview : https://www.adobe.com/products/flash/features.html
Flash CC 2014 Blog Post : http://blogs.adobe.com/flashpro/2014/06/18/flashprofessionalcc2014/
Please try it out the 2014 release and let us know your feedback.