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All paths have to be relative to the site root folder, not your C: drive, then they will run fine both on your home machine an on your server. If you use relative paths, like src="../mystyles.css" it will always work whereever it is.
I had my computer guru over here on another matter shortly after I set up the site last April (it did the same thing then) and he spent less than 5 minutes fixing it so that it worked right. I was so happy that it was fixed that I neglected to write down what he did! DUMB! I have spent over two days researching what might be wrong and finally sent him an Email this morning saying that I had given up. I have not, as yet, heard from him.
If it's a front page created and maintained web, don't use FTP for any forms, webcomponents, and the initial FTP, as sometimes FP gets confused as it didn't actually UL the web - use FTP for pages you don't want FP to realize are in your web.
When adding a link, highlight the text, right click, select hyperlink. This opens a box to somewhere in your web. If your web is c:/my webs/myhomepage/page.html, NEVER browser up past myhomepage to the my webs folder. If you get to the 'my webs' folder, as soon as you do, FP always thinks your out of your webpage and will create a c: link even if you drill back down into your actual webpage.
To fix links, goto reports, and do a validate links report. Sort by link, and then if there is still a c: link, right click it, select the actual link in your web (or add an external link).
Once you have fixed all the links. Recalculate all hyperlinks and double check the report.
If FP links to a c: page, and not a relative or absolute page, when you put your cursor over the link, you will see, c://etc... if it's a relative, you will see the file name or ../myfile, etcc, and if its absolute you will see, ht*p://pagelocation.
If you right click inside most dialogue boxes of FP, you will not see the paste/cut options - you can still use them, but you have to use cntl c, cntl v, etc.
When publishing the web, use FP's FTP the first time, useing FTP later on can be ok. When you goto publish, make sure the published location starts with ht*p://myweb.com and not myweb.com.