Why do the screen flash and scroll bars move when PerfectIt is running?

If you're working with tracked changes, you should enable 'Revisions Mode' (found under the 'Options' section of PerfectIt's 'File' menu). In Revisions Mode, PerfectIt scans your document in a way that may cause the screen to flash or blur. The flashing is harmless to your document. The effect will not happen if you accept all changes in your document before running PerfectIt.