Unfortunately, RM 2003 doesn't have a script editor. Also, I tried making a parallel process that took away hp upon walking, but that still showed the damage flash. Just for the record, Here's my parallel process:
CODE
Branch if Dude Poison Condition
Key input processing (up,down,left,right) [00??:some variable]
Branch if Var [00??:some variable] is 1 or more
Change sprite asoc. (hurt sprite) //optional. just in case you want SOME sort of thing showing that Dude's HP is draining with every step
Change HP: Dude 3 HP remove //amount removed can vary from character to character NOTE: still induces flashing
Wait 0.2 Sec
Change sprite assoc. (normal sprite) //only needed to change it back
End
Key input processing (up,down,left,right) [00??:some variable]
Branch if Var [00??:some variable] is 4 or less
Change sprite asoc. (hurt sprite)
Change HP: Dude 3 HP remove
Wait 0.2 Sec
Change sprite assoc. (normal sprite)
End
And then repeat for all characters that it is possible to get poisoned.
So, I guess until somebody finds a method that doesn't induce flashing, you'll be stuck with the damage flash.
I'm sorry.
EDIT: and yes, I removed the default walking damage on the poison condition before I tested this.