I just upgraded to LR 6 from LR 5.7. When I use the gradient tool now, the tool pulls down in red versus transparent. All the gradient tool sliders are in the 0 position. Color sliders are also 0. I am using a MacPro and didn't have any issues with LR 5+.
Sounds like you have the mask overlay turned on.
See the check box at the bottom of the screen or the Menu: /tools/tool overlay/
On the tool bar simply uncheck Show Selected Mask Overlay.
The graduated filter tool has a new erase brush in LRCC/LR6 so the mask is useful for removing part of the effect where you don’t need it.
Thanks you. The bar menu/tools/tool overlay/ needs to be turned off to use it in the transparent mode. I appreciate your reply.