I am pretty sure you have to change the extension to avi first (I forgot to mention that) But I found these instructions online
1. You should check the QuickTime file’s codec. Open the file in QuickTime, click movie, then choose 'get movie properties'. On the left drop-down menu choose video track. On the right drop-down menu choose format. The codec is listed on the 'data format' line. If it’s a cross-platform codec like Indeo or Cinepak (meaning it can be in either a QuickTime or avi container) then go to step 3. If it’s a QuickTime-only codec (like Sorenson or 'video'), then go to step 2.
2. If it’s a QuickTime-only codec the conversion has to be in two steps. You have to convert it to an avi first, then you can convert it to Windows Media. Your two options are to use QuickTime Pro ($30 from Apple) or Rad Video Tools (free). From some of the posts on the board, it appears Rad sometimes has glitches converting audio; if that happens to you then just get QuickTime Pro. When doing your conversion to avi, I advise choosing a lossless codec or no compression, so that there is no loss in quality. (The avi file may be big though).
3. If you’re from step 1, just feed the QuickTime file into Windows Media Encoder; if you’re from step 2, feed the intermediate avi into Windows Media Encoder. Then just encode!