Magics are all handled from functions that that call makes, NFITC1. The summons, items, enemy skills... everything, most likely (The knights of round is)
00BF23B8
The list of functions that are executed are placed starting there (the function queue as you said). Cure for example, calls 2. One sets things like the "CURE" title bar and text... the rest are the green sprites, called multiple times to generate the effect you see on screen.
Since the counter for the main call can go to 63h, this probably means the total functions that can be called in any one magic is 100.
What I'm thinking is, in order to get these magic effects running at the speed you want, you are going to have to mess about calling the main call 3 of 4 frames (or something) or manually edit the counters(maybe) for each and every function that is called (that would be a nightmare, but I can supply you with the way to find all that get called).
Let me know what you think.
In related news... I fixed the issue with knights of round, but not how I'd like... basically I have to make that call function call all 13 knights' functions. I've done this by comparing the register value to the knights' functions, but only when the main call is being skipped by the pause var. It's a very annoying fix.
So let's take first few knights....
0047ABB0
0047C793
0047CBAE
0048034E
00480776
If the value in the register is 0047ABB0, it will always be called. Thus the knight will never disappear. I have no idea why the knights disappear when the call isn't calling them... and yet other magics that use the same call function do not. (like cure).