We use a scripting language like php, but the file extension is still .htm for the file. The extension triggered it to go through the IFilter and only show a few binary characters and said the file was identical. I disabled the filter, but not sure what would cause it to do that.
Well, I would first check if IFilter works correctly - by trying plain html file. If it works, this is how it handles php files - it's just not ready, I can not do anything here. If it does not work - let me know, and we will try to find what could be wrong.