What platform are you running on? With regard to the Find and Replace tool window, do you normally have it docked or floating all the time, or just bring it up as needed and close after? And by not functioning, is it just the Find/Replace buttons at the bottom grayed out or are all of the controls disabled some way. It would be great if you could grab a screenshot of it if it occurs again so I could see all the active settings.
Is there anything about the project you could share publicly? About how many files are in the project and are there wildcards that define the files for the project?