Using the documentation http://wiki.pmease.com/display/QB50/Working+with+Subversion, we see how to configure an SVN Repository to not checkout externals, and then add a Repository definition for each external working copy to reproduce the correct structure with individual checkout steps. This is the only way to get the commits to the externals listed in the SCM Changes report and also for those commits to be considered in the Build Condition "changes found in referenced repositories."
Well I have a repo with 325 externals, we call it a meta repo, and it's a real pain to manage reproducing the structure with all the individual checkouts in QB when it's already setup in SVN. Why maintain both? It's a real benefit for the developers to have a single checkout to reproduce the full product build workspace. Every SVN client I have used (command-line, TortoiseSVN, SmartSVN) handles reporting all the updated files individually per external working copy when I update the meta repo working copy. It's a very large RCP application that we build with a single Maven reactor using Tycho. We're working on splitting it up but the underlying problem still remains that QuickBuild doesn't support havey use of externals very efficiently.
I've submitted an improvement request at http://track.pmease.com/browse/QB-1444 where a possible implementation and factors limiting the potential to implement it are being discussed. Low votes is listed in the comments as a reason to not pursue this improvement.
So if this issue is relevant to your environments, please go and vote for QB-1444.