The class indeed sets zero parindent and a nonzero parskip. Moreover it uses vmargin which is known to be incompatible with some packages, notably atbegshi which is used by various others.
I suggest you to modify it, changing lines from 66 to 89; here's the original (with line numbers for reference):
66 \usepackage{setspace}
67 \onehalfspacing
68 \setlength{\parindent}{0pt}
69 \setlength{\parskip}{2.0ex plus0.5ex minus0.2ex}
70 \usepackage{vmargin}
71 %----------------------------------------------------------------------------------------
72 % MARGINS
73 %----------------------------------------------------------------------------------------
74 \setmarginsrb { 1.5in} % left margin
75 { 0.6in} % top margin
76 { 1.0in} % right margin
77 { 0.8in} % bottom margin
78 { 20pt} % head height
79 {0.25in} % head sep
80 { 9pt} % foot height
81 { 0.3in} % foot sep
82 %----------------------------------------------------------------------------------------
83 \raggedbottom
84 \setlength{\topskip}{1\topskip \@plus 5\p@}
85 \doublehyphendemerits=10000 % No consecutive line hyphens.
86 \brokenpenalty=10000 % No broken words across columns/pages.
87 \widowpenalty=9999 % Almost no widows at bottom of page.
88 \clubpenalty=9999 % Almost no orphans at top of page.
89 \interfootnotelinepenalty=9999 % Almost never break footnotes.
Here's the modified code
%%% Uncomment the following two lines if you really want doublespacing
%\usepackage{setspace}
%\onehalfspacing
\usepackage{geometry}
\geometry{includehead,includefoot,
left=1.5in,
top=0.6in,
right=1.0in,
bottom=0.8in,
headheight=20pt,
headsep=0.25in,
footskip=0.3in}
\doublehyphendemerits=10000 % No consecutive line hyphens.
\brokenpenalty=10000 % No broken words across columns/pages.
\widowpenalty=9999 % Almost no widows at bottom of page.
\clubpenalty=9999 % Almost no orphans at top of page.
\@clubpenalty=9999 % Almost no orphans at top of page.
\interfootnotelinepenalty=9999 % Almost never break footnotes.
Comments
Double spacing is bad, avoid it if you can.
vmargin is not to be used.
Setting a flexible \topskip is a quite bad idea.
The final settings of the penalty parameters may seem a good idea, but it's not. However, I didn't touch them, except adding the setting of \@clubpenalty, which is the real parameter in LaTeX for controlling orphan lines.
\raggedbottom in a twosided document is not recommendable.