Re: [GUIDE] Flashing ROMs correctly, every time
Most ROMs that you flash have script in the updater to fix permissions for you after everything is installed and sometimes even at boot during the loading phase of the /etc/init.d (right when you are seeing the boot animation)
I wouldn't do it unless your ROM developer instructs you to, or if you are having problems with certain apps force closing on you, or other out of the ordinary issue.
A common example is your market not being able to download an app, or it force closing, things like that. Clearing data on whatever app you are having accessibility issues with, then wiping cache and dalvik cache, then fixing permissions, will usually solve little issues such as these.
Hope that was clear for you.