Today I got bored and pissed off about this problem and quickly found a solution to it. Apparently, it was discussed in NucleusCMS forums in this thread. All I had to do was to make this line from index.php
:
$CONF['Self'] = './';
to look like this:
$CONF['Self'] = '/blog';
Those of you who had problems with posting comments should be now totally satisfied. Search engines should also start indexing better, since there will be no more ambigues URLs. Me, well done.