FlashScan V1 supports logging for all controllers that it supports for tuning. You will be able to log your Allison 5 speed, but you won't be able to log or tune an Allison 6 speed. To get you up and running, below are some suggestions:
Make sure you are selecting LB7/LLY Allison TCM from the drop down list.
Try validating the PIDs for the Allison controller. To do that select the menu option Info->Validate PIDs while connected to the Allison.
There is a not so well known bug in the software that can cause the "validated" PID list to remain as the ECM PIDs even after you tell EFILive you want to work with the TCM. To get around it, after you connect and select the Allison TCM controller, click on one of the column headers in the [PIDs F8] tab page to re-sort the list by that column. Doing so will cause EFILive to refresh the list and disaply the correct validated PIDs for the selected controller.
Let us know how you go. The age of your software shouldn't be the reason why logging won't work, but at some stage you should update.
Cheers
Cindy