This looks to be the correct behavior of the automated ships and crew training skills to me.
The reason that the repair all button shows up when you put an automated ship into storage is the total number of combat ships and automated ships drops, which means the main character skills now provide more CR to the rest, and thus you can repair up slightly higher in terms of CR. However, putting the ship back into your fleet will drop the maximum CR possible again, producing the negative CR per day
In your first screen shot, on the left side of the screen it says "Combat Ships 463" and "Automated Ships 229".
Crew training has reduced effectiveness above 240 DP worth of combat ships, and Automated Ships skill has reduced effectiveness above 120 DP worth of automated ships (including multipliers from alpha, beta, or gamma cores).
So in this case, 240/463 * 15% = 7.78% (round up to 8% in terms of reporting on screen) CR from crew training, and 120/229 * 100% = 52.4% CR for automated ships.
So without that Rampart in your fleet, I would expect ships without combat endurance to have 70+8 = 78% maximum CR. Automated ships have an inherent -100% penalty all the time, which the automated ships skill counter acts partially. So the Remnant and Derelict drone ships I would expect to have 70-100 (penalty)+52 (automated ship skill) + 7(crew training) = 29% maximum CR (44% if you added cores which give combat endurance since that bumps it up by 15%), which seems to match your picture.
When you put that Rampart back in your fleet, your combat ships number will go up to 478, and automated ships will go up to 244. This will drop the bonuses to 240/478 = 7.53% and 120/244 = 49.1%.
So now your maximum CR dropped by 0.3% CR on all your combat ships, and 3% CR on all your automated ships. Since you had just repaired all ships up with the repair all button, they are now losing CR since they are over your new maximum from your skills.
I hope that clarifies the issue.