Why one FLV file displayed but smaller one did not?

Here at work, I accepted an mp4 video file from a client and converted it to flv for viewing online. The company has a license to use Wondershare for this kind of thing. File size went from 193MB to 41MB. However when I checked to make sure it displayed normally, all I had was a black box and the audio. Have never had a problem with this type of conversion in the past using same process. One of my coworkers tried to convert (different software; he's on a Mac) and his flv displays somewhat normally, but is 444MB, causing pauses while the data streams. 
Any way I can diagnose why my flv was audio only? When I compare media file properties, the only difference I can see is that his video stream format and codec ID are Soreson Spark / 2 while mine are Advanced Video Codec / 7.
The URL is proprietary so that's all I can give out.

Well, I tried several alternate FLV encoders. Riva is free and highly touted but won't let me change aspect ratio. The trial version of EasyFLV (I'm not affiliated with any of these companies by the way) got the job done although it was much slower than Riva.
I'd still like to know how to diagnose FLV encoding problems?

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