You have to move the floor through background controllers instead of through animation. They're optional controllers for your stage elements that you can put at the bottom of your def. If you don't know what background controllers are, read near the bottom of the bgs file in the docs. Here's a quick example of what it'll look like, taken from my Ikari Team KOF 96 stage:
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[BGCtrlDef floor]
looptime = 512
ctrlID = 4
[BGCtrl flooradd1]
type = Posadd
y = 1
time = 77, 77
[BGCtrl flooradd2]
type = Posadd
y = 1
time = 129, 129
[BGCtrl flooradd3]
type = Posadd
y = 1
time = 167, 167
[BGCtrl flooradd4]
type = Posadd
y = 1
time = 203, 203
[BGCtrl flooradd5]
type = Posadd
y = 1
time = 255, 255
[BGCtrl flooradd6]
type = Posadd
y = -1
time = 333, 333
[BGCtrl flooradd7]
type = Posadd
y = -1
time = 385, 385
[BGCtrl flooradd8]
type = Posadd
y = -1
time = 421, 421
[BGCtrl flooradd9]
type = Posadd
y = -1
time = 459, 459
[BGCtrl flooradd10]
type = Posadd
y = -1
time = 511, 511