Ah, I understand what is happening with the list. Storing up 900k metal and crystal I can see the issue. Since the cannon is 54,000 m+c/s, it depletes my reserve almost instantly with an income about 2k mc/s. Once the reserve is gone, only every 5 seconds or so will the mini fort that was repairing it will flash onto that list. While it waits for the reserve to build up so it can tick again, the minifort disappears from the list. The interesting part is that if you pause when you have a negative cash flow (like I was), it seems that the list will continue to update. Since the minifort now (on the next tick) will have zero resource flow it is gone. If you sit there and watch, the large negative flow for the fort will flash and correspond to a global negative flow. I do not think you can unpause the game while in the resource flow tab since it was not obvious to me that I should sit there and watch it with the game unpaused.
Now that I understand the issues, I can totally work around it. It was a confluence of issues that caused it to be a problem. I was refleeting after a AI homeworld attack mixed with an exo wave of 2 HK's that dropped in on my main reserve fleet. So the additional resource drain was not unexpected at that point. I did not really notice until about 30minutes latter that I was still not able to have any reserve and tried to figure out why, even after I manually verified that the refleeting was complete and I had paused all constructors. Thanks for the patience with a new player