If you enable a plug-in during full screen playback, Windows Media Player must reset the rendering pipeline to allow the new plug-in to be used. The video has to renegotiate various properties which may be incompatible with the current playback stream. You may experience different behaviors when doing this with different types of video content (WMV, MPEG, H.264, etc.). Whether Windows Media Player allows the plug-in to take effect or not depends on the properties of the pipeline when you switch the mode to full screen.
A best practice is to enable or disable the plug-in before beginning playback. Preferably, this should be done from the Library mode so that you can be alerted via dialog box if playback has already begun. If you toggle a plug-in on/off, you may then see the following message: "If you are currently playing or paused, this change might result in restarting the media from the beginning. Do you want to apply the new settings?"