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You might find that you have downgraded your flash player by cleaning that directory. You can see the versions of your plugins under Firefox by typing into the address bar:
You should definitely be running a version 10.x flash plugin.
I use the per-user libraries to prevent Seamonkey from attempting to run the 64-bit flash plugin. It works for me, but if you are likely to leave old versions in the directory and forget about it, you are probably best off clearing the directory and living with the support that comes in the standard packages which install into the /usr/... tree.
The /home/<user>/.mozilla/plugins directory is a per-user source of libraries which should override the system libraries. Unless you are doing something special, you are probably not going to want to use that directory. On the other hand, if you recall doing a bunch of work on your browser setup, clearing that directory might give you new opportunities for adventure.
On Ubuntu 12.04.2 LTS \n \l (Linux ws18004138 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25 21:22:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux) that I am runningseems that he plugin directory is /usr/lib/firefox-addons/plugins/
To make adobe flash plugin work for me I copy from the extractd plugin "libflashplayer.so" ---->/usr/lib/firefox-addons/plugins/ and /plugin/usr/* ---> /usr/
Although the page is slightly out-of-date now I think it should still be generally accurate.
It's interesting to learn about the MOZ_PLUGIN_PATH variable too. I'd never heard of it. Perhaps it's relatively new? But it's not the kind of thing that's likely to be preset on most systems, although you could use it to define a custom location if you wanted.