I have finally found what was wrong with some plugins (including SK2) on my WP installation. First of all, a couple of times I was receiving the error that running script had exceeded the max amount of allowed memory (which was 8M), while trying to push 14M, so I just increased the number to 16M in the /etc/php.ini.
Second, I have increased the size of the output buffer, which is initially 4096, to 8192. The idea is that output buffer allows scripts to issue headers after (or in the middle) of the content outputting. This is done by buffering the content output, then catching the header, displaying it and then displaying the content. In my case I had a problem: while trying to activate some plugins, I was given a dialog to download the plugin.php file. This behavior was caused by wrong/missing header, because the amount of buffered data was exceeding 4096 bytes. By doubling this amount I solved all my problems for the time being.