I’ve figured it out. The problem is in the “Encoding” listbox. The default “Configured Encoding” is the slowest. Choosing anything other than “Configured Encoding”, even if you pick something random like Korean, will give you good performance.
The other options I have set is “Look in subfolder” and “Use Escape Sequence”. Unfortunately I cannot post my data file. But this is irrelevant. I repeat the search over 1000 files from an open source project and the result is the same.