Something strange here (No message pop up)

[Roy1991]

At times retreating units seem superhuman in their ability to move very large distances. I supposed it's possible that the game is suddenly generating odd bugs like this. More likely it's a case of units either retreating and merging, as professorspatula pointed out, or units retreating out of sight and staying out of sight, or simply wandering off and not showing up for years (thus causing the no Faction Destroyed messages). If it's possible in your version, using the "cheat" that removes fog-of-war is ideal for situations like this.

That might be the cause for the "Enemy army routs" messages not to appear, but it can't be the case with the "Faction Destroyed" messages.

If you take a faction's last settlement, then the faction's destroyed, and thus there are no more units that wander off (in vanilla RTW at least)

[Barbarossa82]

Unless I'm a far more skilled modder than I give myself credit for, this isn't a feature of Vanilla Balance Mod. VBM changes only a small number of text files, which don't affect the (I believe hardcoded) way the game deals with such things as routing.