Using flip4mac to create WMV only 29s of a 10 m clip gets encoded

When using flip4mac to create an WMV file compressor only encodes 29seconds of a 10 minute clip. The same thing happens when I use MPEG Streamclip. I opened FCP to see if there was a break between the clips at the 29s position and I cannot see one. I am using the MOV file that FCP exported, as the source.
I first ran into this issue using MPEG Streamclip, so I bought the Flip4Mac HD and the same thing happens. The preview pane displays the full projet., The In/Out display correctly. duration is displayed as 10m 16f, which is correct, but the finished product is only 29s.
I have to encode to WMV b/c the company is windows based and most PCs do not have the proper codecs for MOV.

H.264 QT is compatible with most all the Windows video player apps I've tested it with.
Compressor 4 is major buggy. In fact, my Flip4Mac stuff doesn't even show up, and I've been using it for years now. Hoping for a huge bug update soon.

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Below is an excerpt from their site and a couple links to info pages there. The extended features are within the free download, but not turned on until you upgrade, however you can try them with limitations:
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Since the error about the disc indicates that the Transcoding has already finished, I think that we can probably rule out the next step, but let's look anyway.
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Using flip4mac to create WMV only 29s of a 10 m clip gets encoded

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