Autocal is giving wierd codes.

That message is just the statistical report of the download. It shows how many messages were sent without error and how many messages were sent that got corrupted between AutoCal and the ECM. All corrupt messages are retried up to 3 times. If all 3 retries fail then the download is aborted and an error number ($XXXX, where X is 4 digit hex code) is displayed on the screen. If no error is displayed on the screen then all retries were successful.

You can control whether or not you see the statistical report by changing that setting using the EFILive V8 Scan and Tune software.

Select [F6: Devices], click the [Read] button to read the current settings from your AutoCal.
Select the [F7: BBX] tab page and uncheck the "Display OBDII retry statistics after Read/Flash is complete." checkbox.
Click the [Program] button to program that change back into AutoCal.

As for why your truck does not start, I don't think that is related to the 6 messages that failed but were retried successfully. Assuming you did not get any other $XXXX error code.
Try flashing the stock tune back into the truck. If the truck starts and runs OK with the stock tune but not with the supplied tune then you should contact your tune supplier for help.

Regards
Paul