Most likely the dekeos developesr will be able to help you better as this is more a dekeos issue then a ispconfig issue. ISPConfig uses a simple apache mod_php setup, there is nothing special with that.
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Another thing I met is that I had to change the php.ini file globally to install dokeos (maybe it's possible to change it on a per user basis but I don't know how).
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you can set this with php_admin_flag and php_admin_value lines in the apache directives field of the website.