Permalink are messed up help.

Hello,

Short Story:
Permalink are messed up getting repeating path names on SOME pages or links in the code:

Example:

http://website.com/wp-content/website.com/themes/images/img/cavica-logo1.jpg

the page name sneaks in there when writing code ( checked by firebug) something todo with permalink?

i have looked and looked for someone having a similar problem , well i have been trying to set up my wordpress template, learned alot along the way but im stuck, its working i can login to admin there is one major issue and thats permalink, or at least thats what i think it is,
I looked into possibility like
1. Permalink is wrong
2. database issue not set up a proper url in htaccess. files

but this very specific and the question is related to the structure or coding:

like if i set my url links to
For Example below:
<script type=”text/javascript” src=”../javascript/jquery-1.7.1.min.js”></script>

NOW i could use ./
or i could use ../
or i could use www.url.com//javascript/jquery-1.7.1.min.js">

and so on. well the problem i have is in permalink i use
/%postname%/

I tried to change it to other suggestions but whats messing me up is if i out like
<script type="text/javascript" src="../javascript/jquery-1.7.1.min.js">

Something is throwing the permalink in there , its not for a post or anything it for me links to images . so if i put even the full url it will come out like:

http://website.com/wp-content/website.com/themes/images/img/cavica-logo1.jpg

I need to figure out whats throwing the extra links or path names in the urls.