Love the mods, I've just updated the buffalo mod, and I'm still seeing a problem with the guppy not being able to submerse more than 50%. When Breaking Ground first dropped, all of my air breathing engines stopped working until I got a new version of one of the Near Future mods. That said, I've removed most of my other mods (43) except for yours, the mod needed for Heisenberg to work, B9 animation, B9 part switch, Community packs (Resource, Category, Tech Tree), Click Through Blocker, both Filter Extensions, Toolbar Control, and module manager. The guppy will now get to 90% submerged. I tried editing the config for the ballast and added an extra 0 at the end to see if the newest DLC changed things. On a different sub, one powered with SAFERs, I was able to submerge to 900M with IntakeLqd at 3281. Somehow its letting it go with a hull pressure of 8,000 even though its listed as a max of 6,000. Dry mass is listed as 6.093.
Using just the guppy, I have to make it hop a few times to get all of the engines underwater, then it will dive, but it won't stay under water unless I'm holding down pitch. The Nose pitches up otherwise, even using the dive computer button. Now
After I put all the mods back in and reloaded, I found that I did not need as much to keep the sub at 900M. About 1600 IntakeLqd. In both subs, I need two engines on the front because the guppy cab acts like its way too buoyant and using the dive computer button on the side with auto trim, I can't keep it level without moving forward and hitting down pitch on the keyboard.
In my testing with increasing the tank capacity of the guppy save file, I had raise the body ballast tanks to 1350 each and get 3920 IntakeLqd in the craft to stay steady at a depth of 401M without having to hold down pitch and have the engines at full throttle. I'm really thinking its something in the new DLC unless its something I didn't try removing
If I can get the log files hosted for you, I will, but I figured I'd bring this up along with my current testing to date. I hope this information helps.