The raid boss target dummies found in major cities are now the Mists of Pandaria dummies, set up for level 90 characters. This means that the boss dummies now have much more armor, so even if your level 85 character is hit-capped and dodge-capped, you will still miss and be dodged by the target dummy. It also means that your physical attacks will do vastly less damage.
You cannot compare your DPS to the raid target dummy before and after patch 5.0.4, alas. So if you thought your DPS went way down, don't worry. It may just be the target dummy change.