Drop Zones have been improved in 10.0.6, so I'm sorry you are having difficulties. Motion Titles and Generators (and I'm sure Transitions) with drop zones now behave as expected -- i.e.: dragging out the effect clip will no longer change the playback speed/retiming of the drop zone media, nor will it be limited to the original length of the effect as it was before; which means, you can drop a clip and resize the template to accomodate the playing length of the clip without sacrificing the timing or a predefined "out point".
There is a recommendation for "best practices" for upgrading to 10.0.6 (http://support.apple.com/kb/HT5550?viewlocale=en_US&locale=en_US). I think it was incomplete (at least it was in my case) because of the preferences issues that came about. You can try to delete preferences, but I ended up doing a complete "fresh" install. I followed these instructions: http://support.apple.com/kb/HT5149 to remove any and all possible problem files.
*My* issue was mainly that none of the text boxes I published from Motion would appear in FCPX. There was also another "presumed" issue which turned out not to be one: Anamorphic Override (apparently ONLY appears for SD media and not for 1440x1080 media... maybe next release...)
So, try deleting preferences first (http://www.digitalrebellion.com/prefman/) and if worse comes to worse (and I hope for your sake it doesn't come to this!): do a fresh install... that should clean up any issues you might be having.
HTH