LyX to Latex conversion problem

Question

I wrote something in LyX and then converted that into a tex file. But when I convert the tex file into a pdf, a huge gap is produced between the last sentence of a paragraph and the next section title like here:

In addition, a large gap is created between one image and another paragraph like the following:

I am pasting here the preamble set by LyX by default:

\documentclass[12pt,twoside,english,refpage,intoc,bibliography=totoc,index=totoc,BCOR7.5mm,captions=tableheading]{article}
\usepackage{lmodern}
\renewcommand{\sfdefault}{lmss}
\renewcommand{\ttdefault}{lmtt}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}  
\usepackage{geometry}  
\geometry{verbose,tmargin=1in,bmargin=1.25in,lmargin=1in,rmargin=1in,headheight=1in,headsep=1in,footskip=1in}
\setcounter{secnumdepth}{2}
\setcounter{tocdepth}{2}
\setlength{\parskip}{\medskipamount}
\setlength{\parindent}{0pt}
\usepackage{color}
\usepackage{babel}
\usepackage{array}
\usepackage{booktabs}
\usepackage{float}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{setspace}
\usepackage[authoryear]{natbib}
\usepackage[unicode=true,bookmarks=true,bookmarksnumbered=true,bookmarksopen=false, breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=true]
{hyperref}
\hypersetup{pdftitle={The LyX User's Guide},
 pdfauthor={LyX Team},
 pdfsubject={LyX},
 pdfkeywords={LyX}, 
 linkcolor= black, citecolor=black, urlcolor=blue, filecolor=blue, pdfpagelayout=OneColumn, pdfnewwindow=true, pdfstartview=XYZ, plainpages=false}
\makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Textclass specific LaTeX commands.
\newlength{\lyxlabelwidth}      % auxiliary length 

Any suggestions on how to reduce those gaps shown above? Thanks in advance.