I\'ve built a web site several times using the default \"allow this precompiled site to be updatable\" however on the most recent compile the website was very broken. After pl
Unchecking the "Allow this precompiled site to be updatable" compiles the .Aspx Pages, not just the code files (.VB/.CS). Leaving it checked allows you to make certain changes to the .Aspx files after it has been deployed without recompiling (ex = move the position of a control or add some additional HTML markup).
After reading your description of the deployment issues it seems more likely that the errors are because IIS needs the App Pool refreshed. On a low end VPS, sometimes it just makes sense to bounce (restart) it if you have that luxury.
Read the following MSDN articles for more information on Site Precompilation.
http://msdn.microsoft.com/en-us/library/399f057w(v=vs.80).aspx
http://msdn.microsoft.com/en-us/library/ms247286(v=vs.80).aspx