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When did first you notice the template.css.css and other CSS files were this way?
We're they looking OK up until now and now they're messed up?
I wasn't suggesting that you start over; as part of the trouble shooting process, creating another database and installing a second copy of the template would give you something to compare it to.
You could then see if the files in the new install looked OK or not.
In most cases it doesn't make a difference whether you apply a template or use the Rocket Launcher, again, it simply helps in troubleshooting.