If the default font height is particularly large, then I could see how it might appear to be aligned to the bottom if you've manually set the height of the TextInput too small to properly display padding on both top and bottom for that font. Flex is very well designed to handle both automatic and manual resizing of components. That's one of the things I always loved about it. However, differences in fonts on different platforms is going to be an issue with any cross-platform technology.
Anyway, if that's the case, your best bet is probably to choose a different font that will render more consistently across multiple platforms.
An embedded font will be most consistent, of course, since you are guaranteed to be using the exact same font on all platforms, and fully rendered by Flash/AIR.
If you need to use device fonts, though, you'll need to either find one that is available on all platforms and renders at a pretty consistent size everywhere. Or, alternatively, you could look for a combination of different device fonts for each platform, where they are close enough that a pixel or two here and there won't make enough of a difference visually to matter.