So the yellow led is not on when it is remote started? If it is not, then that's why you are having shut down issues.
Things to test.. in no specific order.
Turn option H2 ON. If not using an RF-KIT, simply turn H off.
Flash version 70.35.
Test the YELLOW wire. There needs to power there when key is on and when car is remote started.
Must be in PRO mode to manually change firmware or options when connected to the flash link. To get out of wizard mode, click the gear icon in the top right corner, then choose Go to Pro mode.