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Hi I don't know where the problem is in Skinr, but my local dev site got very slow. So i created a new empty site. Copied over all the modules that were installed on the dev site and enabled the one by one and ran apache benchmark against the site. I went from about 200-300ms to 6000ms after enabling skinr. (I'm testing on windows so PHP is already slow on it's own)
I downloaded the 6.x-1.x-dev and the problem was gone.
So I think whatever problem exists in 1.4 has already been fixed, but I wanted to report this anyway. I didn't start debugging 1.4 any further because it looks like the problem was fixed in dev.