My roomate actually found out the problem. The sample .conkyrc file had something that was interfering with it and keeping it on top if added to the boot. Here is my .conkyrc file just in case anyone else is having the same problem:



# UBUNTU-CONKY
# A comprehensive conky script, configured for use on
# Ubuntu / Debian Gnome, without the need for any external scripts.
#
# Based on conky-jc and the default .conkyrc.
# INCLUDES:
# - tail of /var/log/messages
# - netstat connections to your computer
#
# -- Pengo (<email address hidden>)
#

# Create own window instead of using desktop (required in nautilus)
own_window yes
own_window_type override
own_window_transparent yes
own_window_hints undecorated,below,sticky,skip_taskbar,skip_pager

# Use double buffering (reduces flicker, may not work for everyone)
double_buffer yes

# fiddle with window
use_spacer yes
use_xft no

# xftfont Aberration:size=8

# Update interval in seconds
update_interval 3.0

# Minimum size of text area
# minimum_size 250 5

# Draw shades?
draw_shades no

# Text stuff
draw_outline no # amplifies text if yes
draw_borders no
font arial
uppercase no # set to yes if you want all text to be in uppercase

# Stippled borders?
stippled_borders 3

# border margins
border_margin 9

# border width
border_width 10

# Default colors and also border colors, grey90 == #e5e5e5
default_color white

own_window_colour brown
own_window_transparent yes

# Text alignment, other possible values are commented
#alignment top_left
alignment top_right
#alignment bottom_left
#alignment bottom_right

# Gap between borders of screen and text
gap_x 10
gap_y 60

# stuff after 'TEXT' will be formatted on screen

TEXT

${color orange}SYSTEM ${hr 2}$color
$nodename $sysname $kernel on $machine ${alignr}$color${time %l:%M}
${color orange}Uptime:$color $uptime ${color orange} Load:$color $loadavg

${color orange}BATTERY${hr 2}$color
${color orange}Plug/battery status:${color #FFFFFF} $acpiacadapter 
${color orange}Percent Remaining: $color$battery
${color orange}Time Remaining: $color${battery_time}
${color white}${battery_bar BAT0}$color
$color
${color orange}CPU ${hr 2}$color
${freq}MHz   Load: ${loadavg}   Temp: ${acpitemp}C ${acpitempf}F
$cpubar
CPU
${cpugraph 000000 ffffff}
CORE 1
${cpugraph cpu1}
CORE 2
${cpugraph cpu2}

NAME                 PID        CPU%         MEM%
${top name 1}  ${top pid 1}     ${top cpu 1}       ${top mem 1}
${top name 2}  ${top pid 2}     ${top cpu 2}       ${top mem 2}
${top name 3}  ${top pid 3}     ${top cpu 3}       ${top mem 3}
${top name 4}  ${top pid 4}     ${top cpu 4}       ${top mem 4}
${top name 5}  ${top pid 5}     ${top cpu 5}       ${top mem 5}
${top name 6}  ${top pid 6}     ${top cpu 6}       ${top mem 6}
${top name 7}  ${top pid 7}     ${top cpu 7}       ${top mem 7}
${top name 8}  ${top pid 8}     ${top cpu 8}       ${top mem 8}
${top name 9}  ${top pid 9}     ${top cpu 9}       ${top mem 9}

${color orange}MEMORY ${hr 2}$color
RAM:   $memperc%   ${membar 8}$color
Swap:  $swapperc%   ${swapbar 8}$color
$color
${color orange}FREE SPACE ${hr 2}$color
Linux: ${fs_free_perc /}% ${alignr}${fs_free /} / ${fs_size /}
${fs_bar 20 /}
Windows: ${fs_free_perc /media/sda2}% ${alignr}${fs_free /media/sda2} / ${fs_size /media/sda2}
${fs_bar 20 /media/sda2}
Shared: ${fs_free_perc /media/shared}% ${alignr}${fs_free /media/shared} / ${fs_size /media/shared}
${fs_bar 20 /media/shared}
${if_mounted /media/disk}External: ${fs_free_perc /media/disk}% ${alignr}${fs_free /media/disk} / ${fs_size /media/disk}
${fs_bar 20 /media/disk} $endif
${if_mounted /media/BACKUP} Backup: ${fs_free_perc /media/BACKUP}% ${alignr}${fs_free /media/BACKUP} / ${fs_size /media/BACKUP}
${fs_bar 20 /media/BACKUP}$endif

${color orange}NETWORK (${addr eth1}) ${hr 2}$color
Down: $color${downspeed eth1} k/s ${alignr}Up: ${upspeed eth1} k/s
${downspeedgraph eth1 25,140 000000 ff0000} ${alignr}${upspeedgraph eth1
25,140 000000 00ff00}$color
Total: ${totaldown eth1} ${alignr}Total: ${totalup eth1}
Inbound: ${tcp_portmon 1 32767 count} Outbound: ${tcp_portmon 32768
61000 count}${alignr}Total: ${tcp_portmon 1 65535 count}

${execi 1800 /home/username/nwsweather.sh 12570}