If you prefer play your FLV files with Microsoft Windows Media Player instead the player included with aTube Catcher, then you need to install the FLV splitter and ffdshow codec package. You can download them from here:
FLV Splitter (NT/2K/XP/Vista)
After that, right click over your FLV file, and click on "Open With", click on "Change default application", in the next Window you must choose the Windows Media Player application, if it doesn't appear, you must find it on your %ProgramFiles% directory, click on browse and type "%ProgramFiles%\Windows Media Player\wmplayer.exe" (or copy the text but don't forget to remove the double quotes), after click OK, and OK again. After that, Microsoft Windows Media Player will open and play the selected file; if you receive a message from WMP saying "the extension.... blah blah" click "Don't show message again" and click "Yes". All your files will be open with this player.