I noticed that vmoddomlimits doesn't care about a trailing 'M' or 'K' when specifing quotas... Instead of complaining that there's an unknown character in the quota, it silently ignores it. I ended up with a domain with 100 byte quota and 20 byte per-user quota, and only noticed it from the bouncing messages in the qmail-send log.
An example to illustrate what I mean:
$> vmoddomlimits -Q 100M -q 20M example.com
results in a 100 byte quota for domain example.com, and 20 byte default quota for users.
IMO, vmoddomlimits should be changed to accept these abbreviations, or at least complain when I specify a quota and it can't handle it properly - instead of just silently ignoring "invalid" characters.