Im also getting this problem while going to add flash script directly to the HTML in Cute Editor 6.1.
It strips the <object> tag when switch from HTML to Normal mode and then switch back to HTML mode.

 

Original HTML is

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<object
 classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
 codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0"
 width="240"
 height="159">
    <param name="movie" value="flash/FlashFile.swf" />
    <param name="quality" value="high" />
    <param name="wmode" value="transparent" />
    <embed src="flash/FlashFile.swf" width="240" height="159" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" wmode="transparent"></embed>
</object>

 

 

After switching between NORMAL mode and HTML it strips the <object> tag e.g

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<embed pluginspage="http"://www.macromedia.com/go/getflashplayer src="flash/FlashFile".swf width="240" height="159" type="application/x-shockwave-flash" wmode="transparent" quality="high" /></embed>