Hi Mark,
A few thoughts:
If you're having issues with MIDI cues, it's not because of loading. MIDI cues are essentially instantaneous no matter whether they're loaded or not. Auto-loading or pre-loading a MIDI Cue is mostly cosmetic.
Version 3 was not originally designed to auto-load automatically. This was a significant difference from version 2.
When I say "auto-load", I mean "when you press GO to trigger a cue sequence, the next cue sequence is automatically pre-loaded".
In version 2 this always happened. Often it was good, sometimes it was very bad (if the cue sequences were very long).
Version 3 turned this behavior off, but that was not perfect either, because sometimes it is still important to pre-load cues. This is often true with a sequence of video cues that take some time to load.
Thus, the auto-load parameter was added. It allows you to select on a cue-by-cue basis which cues will automatically load when you get to them as you go down the cue list.
Hope that helps,
Chris