I too have experienced this issue, with Flex 3.1 and Flex 3.2. In my case, I've definitely identified the culprit as the Application Builder. I normally edit my config.xml and widget xml files in a text editor, outside of the Application Builder. But occasionally I do something in the App Builder, such as add a custom widget to my project, or add or remove operational layers, and then click the Save button to save my changes. Immediately after saving changes in the App Builder, I open my config.xml in a text editor and I notice that the <height>, <witdth>, and <preload> tags for some (not all) of my widgets have been either removed or replaced with default values. In particular, this frequently happens to my TOC, Print, and Navigation widgets.
This happens so often that I have taken to saving backup copies of my <widget> tags in my config.xml file (the backed-up tags are commented out with <!-- --> so that they don't interfere with the normal operation of the web map). The backed-up tags don't get altered when I do something in the App Builder, so that way I can easily recover my custom <width>, <height>, and <preload> tags when the App Builder sets them to the default.
But I have no idea why the App Builder is resetting some widgets to default values for <width, and <height>.
