The RS3 8V suffers from heatsoak, the standard intercooler really struggles to keep intake temps under control if you have been sitting in traffic for a while, or even giving it plenty of full throttle runs between roundabouts on the local ring road (if you know what I mean). If the ECU sees intake temps rise over a certain temperature it will reign in the power to protect the engine, which in turn will make the performance feel flat. When you add a re-map, the extra performance only adds to this problem which is why an uprated intercooler is an essential adition to a tuned engine on the RS3.
There is another little foible too. The boost control on the RS3 can be a bit flaky and tends to be a bit erratic sometimes, its possible that your re-map may be highlighting it due to the extra power and torque demand in mid range. Most good tuners can smooth this out when doing a live custom map on a dyno. If you have gone for a 'plug and play ' and drive away jobbie then you will not have had the benefit of this.