ESP RF Test Tool v2.8 incompaitibility issue

[HT_espressif]

We are using the automatic programming feature with the uart port on our ESP32-C3 board. (RTS and DTR pins)
When developing in the IDE or uploading binaries it all works fine but we have a problem when using the RF test tool.
We can upload software just fine but we cant send commands once the software is loaded. It seems to be stuck in the download mode.
To fix it I have to detach the DTR and RTS connection when sending commands. And it will work.
Is there a way to get it to work with these wires attached?