<p>Ok, so I have VS 2008 and SVN. When I "rebuild all" a handful of my .dll's disappear from my bin folder. </p>

<p>I have these .dll's in a library folder and that's where I am referencing them from. </p>

<p>When I go to publish the app the publish fails, I think they are related. When I reboot my web.config (change something and save) this error goes away. However, the publish still fails. </p>

<p>When I go to the folder and update svn puts all of them back of course, but then it just happens all over again.</p>

<p>Thank you. </p>

Sounds like the build procedure removes the contents of your bin directory on build.
I don't understnad where you say you are referencing them from the library folder- and they also exist in the bin directory.
Your publish could be failing for other reasons- it is most helpful to post the errors.
Updating SVN reverts the files to the latest version- so if you have no file, the latest version is the one that exists in your repository.
Things to check:
You are probably receiving errors on your build- it sounds like the DLL's are actually output from other projects in your solution, so you should check if they are building properly or if they are being output to a different directory instead of your bin folder.
Your subversion repository probably shouldn't have any binary or intermediate files such as dll, lib, exe, suo, ncb, and some others but those are the main ones.
Post more details here- from the sound of it, it seems you may be overlooking errors that you didn't post here.