my educated gues would be that searching within a thread is only allowed for a specific group of users, as usually you should be able to see it in the sourcecode if it was just a display/css error.
also i'm wondering why this board is still running vbulletin 4.1.3? i hope that you didn't update for a reason but fixed the exploit manually?
Yep, it may only be set for certain UserGroups... I will check on this later today and add them all if so.
As for the version, it's because not all templates are modified when we do the interim patch updates. Our ACP shows the current version we are on which is the latest though.