Now to your questions about the “Wet / Dry Mixer”. You did not provide any clues as to your User Algorithm connections so I used the standard Factory Algorithm 29 “No Digital” to simulate your problem.
Factory Algorithm 29 includes the standard chain of analog effects (Compressor, Distortion, Analog Graphic EQ, Master Volume, External FX Loop, and Stereo Noise Gate). This analog chain is included in all algorithms, whether they are Factory or User Algorithms. At the end of the algorithm chain, Factory Algorithm 29 includes a Wet / Dry Mixer so Factory Algorithm 29 should be identical to your User Algorithm.
I tried various “External FX Loop” settings and played with the “Wet / Dry Mixer”. I could not replicate the problems you are having. I can only conclude that the connections between the modules in your User Algorithm are not correct.