Hi Mike,
I can see you've already had good information about this but just adding something.
The traces information is stored using Apache Lucene and there are tools that can be used to review the traces data outside APM itself.
If you take a copy of the traces folder and open it up with the lukeall jar file (linked below), it will show the data in a text context that may give you another way to sort where so much data is coming from
luke - Luke - Lucene Index Toolbox - Google Project Hosting
This is a screenshot from the first page when the tool loads up, by selecting a name, in this case 'type', then clicking on Show top terms, it shows you what type of trace is prevalent. If it is a case with a lot of MQ traces, you would possibly see a lot of the MQ correlation values as a value to search on.
I would only do this on an offline copy of the traces data.
For the types, errorsnapshot is any type of error (including stalls), whatsinteresting are the what's interesting baseline type views where a process CPU might have changed, for example, sampled are traces taken from automatic sampling, and normal are traces taken by manual transaction trace sessions.
Regards,
David