GM LS 5.3 VORTEC won't rev past 1500rpm when trans in manual mode

So we have a 1992 Nissan 240sx with a 1999 GEN3 LS type 5.3 vortec, drive by cable setup. We installed the ECM, simply unlocked VATS so it would fire up to confirm it runs. After that we modified some small things, Torque management, Trans type, PE tables, Knock tables and then fired it up, it wouldnt Rev past 1500 rpm, as though that was its rev limiter. I reloaded stock tune and it revs to the moon and works perfect. I then made my changes one at a time to see what was causing it and found that when I changed the Trans type to Manual that is when it would not let it Rev past 1500rpm, switch it back to the stock 4L60E and it revs perfectly fine. Has anyone run into this and is there something i'm missing? Thanks

I should mention we are using HP Tuners for the reflash software

Terminator6742, I am assuimg that the vehicle it is currently in is a manual?

Have you checked your rev limits under fuel/cutoff?

Did you connect to the scanner and check for codes? Or log your gear status and see what it states. You might find that you will have to go in and turn off several fault codes related ti auto trans or tcm

Maybe put up a copy of the tune file and I am happy to have a look.