Try substituting something like this...

if (( ($cylBBox[0] < $cubeBBox[0]) && ($cylBBox[3] < $cubeBBox[3])) && $boundingCheck)
{
print "whatever";
$boundingCheck = FALSE;
} else {
$boundingCheck = TRUE;
}

I think that should do it....
(been a while since I've messed with expressions in maya).