- mixing incorrectly interpreted non-square pixel aspect ratios with square pixel footage
- extreme anamorphic comp settings (if e.g. you are creating a web banner)
- general lack of "space" by using very small transform values for your 3D items
- "Collapse Transformations" used in a 3D comp and intermingled with certain 3D-ish effects or 2D layers that use the same switch for continuous rasterization
- 3D matte modes
- last but not least, of course parenting the camera to scaled Nulls
As you see, this is quite complex, so the only way to nail that sucker is to sift through all your layers and check for the described issues.
The FLV error is most certainly unrelated to the other issue and would point to a damaged install. Bay all means you should use the FLV render from the Render Queue, not the QT plugin found under the "Export" option, so maybe you can try that.
Mylenium