Shooting in to the sun is NEVER good. Throws the camera way off. You want the sun to the side or behind you.
Best times for any photography - drone, DSLR, etc is close to sunrise and sunset. Mid day is typically horrible unless very overcast.
Know nothing about the software you're using - so no help there.
shooting into the sun is often the best light. It makes for the most dramatic photo. It is more challenging though. There is a solution for his problem. In Lighroom, under lens corrections, check "enable profile corrections", turn the distortion slider all the way down, leave the Vignetting slider in the middle. There are also Blending mode options in Ptgui Pro that can help. Also, shooting your panos with a larger overlap reduces the effect, since you are using data closer to the center of the frame, and not using the edges. If by "throwing the camera off" you mean the dynamic range of the scene is too great for the camera, you can use Auto exposure bracketing mode on your drone, with HDR blending in Lightroom to capture a wider dynamic range, including scenes with extreme dynamic range.
