I agree with you on this one, Quicktime is not an amazing product, but it does its job.
If you're not thrilled with Quicktime, Pro will not throw up much excitement either.
There are alternatives to using Quicktime Pro to convert between video formats.
To convert your .mov video files into .wmv you can use the following convertor:
ALO Video Converter 1.6http://www.download.com/ALO-Video-Converter/3000-2194_4-10566330.html?tag=lst-0-7
ALO Video Converter is a simple and easy-to-use converting AVI, MPEG, MPG, DAT, RM, RAM, RMVB, MOV, ASF, WMV to AVI, MPEG, RM, WMV. PAL/NTSC conversion and vice versa are available. It can handle and convert between the following formats: AVI, MPEG, RM, MOV, ASF, WMV. Full Drag and Drop is supported. The app features Fast conversion speed: video format conversion is performed directly without any temporary files, and thus enables high converting speed and economy of hard disk resource. Batch video files conversion is supported.