MS is really finicky for stuff like this. Do this:
- start a new project in TS called 2.1.1DIYTune, select 2.1.1 from the ECU list
- load the DIY tune in with no errors (if you get errors, start over, select the right ini)
- open ANOTHER window of TS
- start a new project called 3.0.3uLive
- reburn the 3.0.3u firmware
- open the 3.0.3live and connect to the MS unit. should have no conflict
Now, manually go from the 2.1.1 TS window to the 3.0.3u TS window, copying any setting you can. You now have a stable 3.0.3u base tune.
The alternative is to load the 2.1.1 firmware. Loading MSQ with 3.0.3 firmware may lead to table corruption (ask me how I know) and this is the ONLY truly safe way to do it.
You can export and import the VE, Spark and AFR tables so you really only have a few screens; its not that bad.
I'd do this over running 2.1.1 anyday, as 3.0.3u has quite a few fixes in place.