it turns out that you should never use a battle chance greater than 31 in the field encounter list. 32-64 are bugged because the signed number is not calculated correctly.
There are 5 examples of this glitch occurring in the Vanilla Game. The effect isn't that the battle will play out incorrectly, but rather, the battle check will cease to continue, and every formation placed after
the formation with >31 enc rate will be ignored. This is why we will never encounter: (formation IDs are in dec)
mtcrl_4 - #505 2x Cokatolis (Mt. Corel Rollercoaster screen)
mtcrl_9 - #514 1x Bagnadrana (Mt. Corel Bridge)
mtnvl3 - #585 2x Sonic Speed (Mt. Nibel Bridge)
junsbd1 - #762 2x SOLDIER:2nd (Red Submarine Dock past barking dog)
junin2 - #945 2x SOLDIER:2nd (Outside press conference room, during escape).
I have written up on this glitch, along with several other similar glitches within the Bug Report section of my Enemy Formation Charts.
Look in Section E - Final Notes, although I believe White Wind may
have tracked them all in the bug tracker. It's still worth checking.
In regards to the battle with the pyramids, are you sure that you didn't have encounter "0" set with an encounter rate of >0? I've done it myself in the past, the likely culprit is when editing the four "special battle" slots.
One other thing worth mentioning for those that didn't know, the total encounter rate for all 6 "normal battle" slots must
total 64, otherwise the game will just freeze as soon as you try to traverse on it.