The solution is to raise the limits or set them as inactive. If you continue hit a limiter, check the map for the proper settings.
If the map slot that was set to 6900 was configured as "Active" and the map slot was changed in car, there would be no way for it to achieve a 2500rpm limit unless the primary rev limiter was set to 2500. It sounds like either the number of Active Map slots was set lower than where the 6900rpm limit was, or another limiter was set to 2500rpm. Also, each of these settings must have the configuration enabled at "1" before they will become active in map switching.
If anyone is going to be using a 2WD dyno with an OTS map file, you will be limited to 6500rpm on the dyno as we have default the factory "launch" limiter to 6500 as an over-rev protection. This is still high enough to see the available powerband as power falls off well before this engine speed. We can certainly eliminate this default and set it back to 6900rpm if that is desired. If you are using a custom tune, you will need to ensure the appropriate settings are enabled to allow sufficient RPM for your dyno pull. This would be as simple as setting a map slot to have mirrored rev limits on the LC and Primary tables.
This forum thread may be helpful: http://www.focusst.org/forum/cobb-tuning/18974-new-lc-causing-dyno-run-issues.html#post366535