Exporting Cross Platforms/Windows Media Encoder

(I know this is an apple forum, but I have transferred videos across platforms from a Mac to a PC. My employer wants me to create wmv files to play on windows media player and all the other forums told me to cross platforms if I couldn't pay for a program to export through Final Cut Pro.)
Long story short, I exported out of FCP into M2v files. The files are now on the PC, where they play fine. However, when I try to convert into wmv, I lose the first 3-4 seconds of video and it throws the audio off by that much. Am I doing something in Windows Media Encoder to lose that or was the initial transfer from FCP the problem?
Any help would be great.

No answer from me about what to do on your PC, but you might go directly from FCP to WMV using Flip4Mac in trial mode. It will give you 1/2 the duration of a clip, up to 30 seconds, so you can test whether it works for your purpose. Could be worth chunking out the $49. for the license.

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