OK, had a further think about it, and realised why the cursor based videofx in the first attempt wasn't working. This was because the Next Click Action had a target of self, so the source and viewer are set to create on the same window. The target on a Next Click Action needs to be something other than self, as the window that runs the action is the window the Viewer gets created on. The problem is that when doing round robin, you want self to be in the target group so it cycles around, just like the keystroke action.
This does make it a little tricky to achieve currently (it could work with changes in ISBoxer, but that particular area is a little complicated so unlikely until ISB2 comes along). Also, your original description does appear like you are experiencing an oddity in the VideoFX that some people get, and this is all just a workaround for it (actually its the WinAPI not quite doing as advertised, but only happens for a select few people, not sure why at this stage).
Anyway, here goes. N.b. Delete the previous Special key map first. It'll make this go much easier (also, if it loses references on the steps, paste it, then paste it again, selecting Replace existing item)
https://pastebin.com/raw/cbBFuwnYNow, this key map contains a bunch of step synchronization mapped keys. It also "double binds" the same hotkey, BUT, it is setup so those double bind mapped keys are disabled by default, and then ONLY LOADS ONE PER SLOT, so the double binding doesn't end up with more than one mapped key on the same bind active on the same slot.
The "X + Next Click SLOT X" mapped keys are basically individual round robin setups that are to be used on each slot. I've set them to start disabled by default.
The idea is that each slot will load the appropriate mapped key, and will cycle through it. So the round robin works, and maintains the cycle when you switch windows, it also will sync the other mapped keys, so if you are on slot 1, press the hotkey twice, then move to slot 3, then Slot 3 will be the next to fire. You press the Hotkey, move back to Slot 1, and Slot 4 will be the next to fire.
You may need to adjust the vfx cursor size, which unfortunately means 20 edits.
To get it to work, you need to run the "Load X + Next Click for Slots" mapped key (err, and assign it to the character set, but you figured that out before... ). For testing, I'd put it on a hotkey. For realz, I'd put it in the Character Set loaded/reloaded (if you have a mapped key here already, then I'd add it into that one as a Do Mapped Key action).