Here is the quick answer so you can hopefully get on with your day of debugging goodness.
Use Error
rather than Info
level logging.
System.Debug(LoggingLevel.Error, 'For the love of god, show up in the log!'););
You don't need to use "Set event filters for username" under Monitoring > Debug Logs > Filters. Just have the developer console open and set the ApexCode level to ERROR.
When you look at the Change Log Levels screen in the developer console what you are actually seeing is a UI over the TraceFlag records.
There are two records due to the two TraceFlag records that get created when the developer console is started. One will have the ScopeId set to the current User and the other will be empty for organization level logging. Note that it is also possible to create multiple traces for a single user, which results in multiple rows in the UI. Further rows can be created where the TracedEntityId is that of an ApexClass with LogFilter overrides (see below).
It might be worth checking for rogue records here. You can do this with SOQL in the Developer Console Query Editor by checking "Use Tooling API":
Select Id,IsDeleted,TracedEntityId,ScopeId,ExpirationDate,Workflow,Validation,Callout,ApexCode,ApexProfiling,Visualforce,System,Database from TraceFlag
You can safely delete them all (assuming you are the only dev in the org) and then let the developer console recreate them.
It would be worth checking if you have per Apex class logging level overrides on. This would appear under the Log Filters on the individual Apex Class.
If you are interacting with Salesforce via an external tool or the API it is possible the requests are overriding the logging levels. For instance, the DebuggingHeader in the older Apex API allows the logging levels to be explicitly set for that request.
As you found, Workbench offers the option to execute anonymous Apex with defined logging levels.
The FuseIT SFDC Explorer tool lets you explicitly define the logging levels that will be applied. (Full Disclosure: I work for the company that makes this tool)
Best Answer
I can confirm that this indeed happens inside namespaced packaging orgs (= the developer org of a managed package).
I have the same problem with two of our managed ISV packages. Even setting the Debug Logging Level to ERROR everywhere (assumption 1: Log reaches max size otherwise and skips my debugs) or setting it to FINEST (assumption 2: I should see more then) did not change anything.
This happened imediatelly after the Summer '13 Release.
I opened a case with Premier Support but I did not a response for weeks and regularly escalate it.
I thought I post this as an answer so I can use comments to keep you updated.
UPDATE 1: This only happends in Testclasses where I have many (20) test methods. Maybe thats the reason why the logs fills up with MUST SHOW stuff.