[Samsung Galaxy Nexus] molesarecoming:
might be your editor. properties conf is a system file, should it get corrupted its the same fallout as a corrupted build.prop. goku over in the s3 forums figured that some editors can do that, root explorer for instance. he got instant bootloops. after he used solid explorer it worked again. also make sure the file is not broken, watch out for line breaks or anything unusual. its also name value pairs, name.blablabla.suffix=value

for now, just wash the rom over and it will boot up again. you dont loose anything but your properties. then try again with SE.

you can also make yourself preferences for the launch section. these can even survive a flash if you store them in /data/data/com.paranoid.preferences/files --- just copy /etc/paranoid/prefrences/2_pref.xml, open it and cut out all the dpi and system configs. when you apply it in paprefs it should in theory only add colors and not overwrite properties.conf

edit:

there you go

<property name="My colors" active="true">

<description><![CDATA[
.........................................................
]]></description>
<setting type="Hybrid" target="com.skype.raider.nbcol" value="ffffffff"/>
<setting type="Hybrid" target="com.skype.raider.nbctrlcol" value="ff00c1ff"/>
<setting type="Hybrid" target="com.skype.raider.nbglowcol" value="ffffd400"/>
<setting type="Hybrid" target="com.cyanogenmod.trebuchet.nbcol" value="aa000000"/>
<setting type="Hybrid" target="com.cyanogenmod.trebuchet.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.cyanogenmod.trebuchet.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.sand.airdroid.nbcol" value="ff6b9900"/>
<setting type="Hybrid" target="com.sand.airdroid.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.sand.airdroid.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.browser.nbcol" value="ff2c2c2c"/>
<setting type="Hybrid" target="com.android.browser.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.browser.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.calendar.nbcol" value="ffc2db00"/>
<setting type="Hybrid" target="com.android.calendar.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.calendar.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.chrome.nbcol" value="ff393939"/>
<setting type="Hybrid" target="com.android.chrome.nbctrlcol" value="ff00ceff"/>
<setting type="Hybrid" target="com.android.chrome.nbglowcol" value="ff656565"/>
<setting type="Hybrid" target="com.s0up.goomanager.nbcol" value="ff000000"/>
<setting type="Hybrid" target="com.s0up.goomanager.nbctrlcol" value="ff00c9ff"/>
<setting type="Hybrid" target="com.s0up.goomanager.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.apps.docs.nbcol" value="ff242424"/>
<setting type="Hybrid" target="com.google.android.apps.docs.nbctrlcol" value="ffe3ff00"/>
<setting type="Hybrid" target="com.google.android.apps.docs.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.dropbox.android.nbcol" value="ff0063b2"/>
<setting type="Hybrid" target="com.dropbox.android.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.dropbox.android.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.facebook.katana.nbcol" value="ff123a6d"/>
<setting type="Hybrid" target="com.facebook.katana.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.facebook.katana.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="flipboard.app.nbcol" value="ffdbdbdb"/>
<setting type="Hybrid" target="flipboard.app.nbctrlcol" value="ff383838"/>
<setting type="Hybrid" target="flipboard.app.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.vending.nbcol" value="ff3b3b3b"/>
<setting type="Hybrid" target="com.android.vending.nbctrlcol" value="ff95a939"/>
<setting type="Hybrid" target="com.android.vending.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.gm.nbcol" value="ff464646"/>
<setting type="Hybrid" target="com.google.android.gm.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.gm.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.googlequicksearchbox.nbcol" value="ffe4e4e4"/>
<setting type="Hybrid" target="com.google.android.googlequicksearchbox.nbctrlcol" value="ffadadad"/>
<setting type="Hybrid" target="com.google.android.googlequicksearchbox.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.apps.plus.nbcol" value="ff505050"/>
<setting type="Hybrid" target="com.google.android.apps.plus.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.apps.plus.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.imdb.mobile.nbcol" value="ffffd500"/>
<setting type="Hybrid" target="com.imdb.mobile.nbctrlcol" value="ff5c5c5c"/>
<setting type="Hybrid" target="com.imdb.mobile.nbglowcol" value="ff000000"/>
<setting type="Hybrid" target="pl.solidexplorer.nbcol" value="ff0ca4c0"/>
<setting type="Hybrid" target="pl.solidexplorer.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="pl.solidexplorer.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.soundcloud.android.nbcol" value="ffff5100"/>
<setting type="Hybrid" target="com.soundcloud.android.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.soundcloud.android.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.verge.android.nbcol" value="ffe00c0c"/>
<setting type="Hybrid" target="com.verge.android.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.verge.android.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.youtube.nbcol" value="ff000000"/>
<setting type="Hybrid" target="com.google.android.youtube.nbctrlcol" value="ffff0000"/>
<setting type="Hybrid" target="com.google.android.youtube.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.talk.nbcol" value="ff464646"/>
<setting type="Hybrid" target="com.google.android.talk.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.google.android.talk.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.whatsapp.nbcol" value="ff2e9e00"/>
<setting type="Hybrid" target="com.whatsapp.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.whatsapp.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.twitter.android.nbcol" value="ff009ecb"/>
<setting type="Hybrid" target="com.twitter.android.nbctrlcol" value="ffffffff"/>
<setting type="Hybrid" target="com.twitter.android.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.contacts.nbcol" value="ff000000"/>
<setting type="Hybrid" target="com.android.contacts.nbctrlcol" value="ff00c0ff"/>
<setting type="Hybrid" target="com.android.contacts.nbglowcol" value="ffffffff"/>
<setting type="Hybrid" target="com.android.settings.nbcol" value="ff000000"/>
<setting type="Hybrid" target="com.android.settings.nbctrlcol" value="ff00dbff"/>
<setting type="Hybrid" target="com.android.settings.nbglowcol" value="ffffffff"/>

</property>

copy, paste into anyname.xml, move to /data/data/com.paranoid.prefrences/files/, make sure its has read and write permissions, restart paprefs - it should appear