Hi,
Does it happen in all web browsers?
Does changing the skin affect the issue?
One thing to keep in mind when working from svn trunk is that the skins in your site at /Data/Sites/1/skins do not get updated by svn updates. So periodically you may want to delete the skins from /Data/Sites/1/skins (except for custom ones) and copy the ones from /Data/skins into /Data/Sites/1/skins. However, you don't want to copy the hidden .svn files so you should right click the /Data/skins folder andchoose TortoiseSVN > Export and choose a place for it to copy the files, this will give you a clean set of skins with no .svn files and then you can copy these into /Data/Sites/1/skins.
If using custom skins you may want to periodically compare your skin to the latest included skins. For example if you've been updating from svn for a long time maybe you don't have the ScriptLoader control declared in your layout.master, you should copy it from an included skin.
Hope it helps,
Joe