I hope someone can help figure this out-- I have a working Drupal 6 sandbox on Linux Mint 13 (drupal 6, apache, mysql, php) and I use drush sql-sync to keep my DBs synchronized. It works perfectly.
I tried to replicate it on a second Linux Mint 13 PC, same configs (vhosts, settings.php, same drush aliases), and drush sql-sync fails every time at the point where it should operate on the local copy of the DB, and then it prints the site HTML 404 page. I copied all the output of the commands on both systems- here are the bits where they differ. This is from a successful run on the first system:
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/var/www/stage $ drush -dvvvvv sql-sync @remotesite @localsite --no-cache --sanitize --no-ordered-dump
[snip]
Calling system(mysql --database=stage_local --host=127.0.0.1 --user=root --password=password --silent < /tmp/stage_local.sql);
Drush bootstrap phase : _drush_bootstrap_drupal_root() [845.82 sec, 7.16 MB] [bootstrap]
Initialized Drupal 6.28 root directory at /var/www/stage [845.82 sec, 8.21 MB] [notice]
Drush bootstrap phase : _drush_bootstrap_drupal_site() [845.82 sec, 8.22 MB] [bootstrap]