There are a number of sniffs which currently walk the token tree presuming that code complies with the WP code style rules.
The net end-result of this is that the messages from these sniffs will not be thrown for code which does not comply with the WP code style rules.
As VIP plugins as well as themes generally don't have to comply with the WP code style, but do have to comply with a lot of best practices, this means that important messages might be missed.
As a secondary result, it also means that an initial run against the WP rulesets might not show all messages and new messages might start to get thrown only once code style issues have been fixed.
I would suggest we should review all (non-code style specific) sniffs for these kind of issues and improve them where necessary.