Hmmm... i've never had this problem before but i think i know what your talking about.
First of all click on one of your local web site files and look in the inspector. The 'Publish' status should be "Always". All your local web site files should be set that way unless there is some reason you don't want them uploading.
Now connect to publish server. In the locked column all folder should be "rwx r-x r-x" and files should be "rw- r-- r--". (There are a few exceptions to this, such as PHP scripts that need execute privelages to work.) If anything doesn't have the right settings select the file(s) and in the inspector click the "FTP Access" tab. Folders should have checks on all read settings, the owner write setting, and all execute settings. Files should have checks on all read settings, and owner write setting only.