Load the subtitle into Subtitle Edit -> "Synchronization" -> "Point Sync". Compare line 100 (usually the first conversation in the prison yard) and line 5,000 (the final escape countdown). If the offset changes, your index is corrupt.
Avoid random open indexes. Use OpenSubtitles.org or Subscene with verification filters—they are free, safe, and genuinely verified by the subtitle community. index of prison break season 1 english subtitles verified