That sounds something like there's a missing indexes or incorrect indexes. Are both apps having problems being slow or just MRBS? Is there anything about any particular queries that failed in some error log?
Without having more data on the size of the tables and how old the app is it's hard to say for sure. You could try turning on the slow query log and see what it logs and then EXPLAIN and ANALYZE to see what it is doing. Then create indexes for those queries.
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