When I enable wobbly windows,the desktop doesn't work right like on 12.04. The workspace is glitchy when you grab a window and that is distorted when you don't close the window. The right click also has the effect which I think is not suppose to. The close animation does not work right when you are using flash player like on a youtube video or other video based. I was changing the launcher opacity when I noticed the second problem. Is there a way to update or fix these?
Unity is not really designed with heavy tweaking in mind, and the version of ships with Ubuntu is heavily patched. I used to modify compiz behavior quite a bit (adding a lot of customization to the tiling behavior + changes to window rules), but it now it breaks stuff pretty badly. It seems like the more compiz is patched (which it is extensively in every release cycle), the more things break when you change the settings. While I am a fan of Unity and enjoy using it very much, it is not a good option for those who would like to deeply modify window manager behavior.
This is one of the reasons there was debate in the last release cycle about removing CCSM from the software center entirely and moving it to a PPA only. Tweaking Canonicals version of Compiz simply breaks Unity, and is discouraged.
If you turn off the Unity plugin in Compiz, some of the other tweaks become more functional, but another distro would be more suited to getting classic compiz behavior. Unity and normal Compiz should be considered different window managers for all practical purposes.
It is also worth noting that the developer of Compiz is no longer working on it so he can focus on his studies and because he believes maintaining a compositing window manager is redundant with Wayland just around the corner. Not sure what Canonical will do after that, but I do recall that they were paying him to put the Compiz functionality required by Unity into plugins that could be ported to Wayland.
Things do not bode well for the future of wobbly windows under Compiz, though I'm sure someone will implement them in Wayland at some point (still having trouble figuring out why anyone would want to waste system resources and battery life on something like wobbly windows, but I'm sure you have your reasons).