There should be no significant differences testing a website on locahost.
Two possible causes:
If your webpage contains any significant AJAX then it's possible that the page never appears to be fully loaded so WatiN just keeps waiting.
I have fixed one or two bugs in WatiN now and then related to detecting that a page has been fully loaded. You might try grabbing the WatiN trunk source and building a fresh copy of the latest code.
If none of that helps, WatiN also has "NoWait" variants of several actions like clicking. You can also override what it means to WatiN to wait for a page to be complete by registering a WaitForComplete handler.