Encoder - poor quality video

I'm having a problem with screen capture videos that I'm using Articulate Encoder '09 to convert from either Movavi Video Suite (I've tried a lot of formats: wmv, avi, mpg, mov, etc.) or Snagit. The quality of the initial video is good, but once I convert to flash (using Articulate Encoder), the quality decreases to an unacceptable level. I am using the Articulate 09 suite, and I publish to an Articulate Online site. I have used Articulate Encoder for other videos (taken from a video camera), and the results have been usable, but these screen capture videos become so fuzzy they just look terrible.

If I convert directly to flash from Movavi, the video quality is much better (also the file size is larger), but sometimes when I upload to the Articulate site, those videos won't play, despite the fact that they work when I preview it in Presenter. I can also get usable flv videos from other programs, such as Wondershare, but they won't play at all in Articulate. Maybe there is a setting somewhere to add a different codec to the program? I don't know.