Also:

Scuba Recon wrote:... The current one I've made I suspect I made the ballast size too small as once one or two rooms become flooded the sub cannot stay on course.

It seems you don't understand how ascending-descending works.

In short: ballasts don't matter. What matters is how much of the sub is flooded.

If the sub is flooded by exactly 7% of its total hull volume - it stays neutrally afloat, you push it down - it travels down at constant speed, you push it up - it ascends at constant speed.

If the sub is flooded by less than 7% - it starts accelerating up, when the sub is completely clear of water it accelerates up at a maximum speed. It doesn't matter if your sub is one big ballast or if it has no ballasts at all - it will not accelerate faster.

On the other hand, if its flooded by more than 7% - it accelerates down, and the more water it has the faster it accelerates. Obviously, if your airlock is more than 7% of total hull volume, then no matter how big your ballasts are your shuttle will always sink when the airlock is flooded. If those two rooms you've written about take more than 7% of total hull volume then the sub will always sink no matter how big your ballasts are, even if they take all the space outside those two rooms.

Making ballast take exactly 14% (btw 1/7 is close to 14%) of hull volume makes its neutral level exactly 50% - your sub will keep its vertical speed if its half-flooded, and a fully flooded ballast will accelerate your sub downwards as fast as it accelerates it upwards when its completely empty. Making a ballast bigger won't allow your sub accelerate upwards faster - it will only allow it to sink much faster and move it neutral level from half-flooded to a lower level.