I had the same issue, scan the car and check for codes if nothing shows up then its the tune. My tuning company said that on the mk6's (newer ecu's) they have a safety cut out on the injectors, all you need to do is go and send your logs to your local dealer and have them forward the logs to the tuning company. Basically they are going to flash your car with the same software but they will remove this ECU behavior so you have no gap between gears. I had to do this plus clear a fuel rail pressure system too high by replacing an o2 sensor, fuel sensor and fuel pump (after replacing the fuel pump it stopped throwing codes). Be careful though and take it easy on your transmission.