To avoid having issue on your first "Start" when you open your APBi (even with auto-login active). Login manually first, and THEN start. It did help me out since i do that.
And yes, this was suggested many time, and should be consider, collection all first, in the same cycle would be solving alot of issues. Expect people to be IG sometimes, and launching their craft, it might not be the same as the Saved cycle on APB. Which means, having 3 Battle Undead on the first 3 slots in your saved cycle, but you still have one running, or even not collected yet on your 6th slot, it will still count as 1 of 3 allowed. That is why, collecting all first is a better option and solution.