Inconsistent results with Version 3.5?

[Lightoscope]

I have two identical runs, with the sole difference being that in the first (runCalc) I have GAPIT calculate kinship (parameters below) and in the second (runKin) I instead use the kinship matrix calculated during runCalc. I had assumed these would produce identical results, but runKin is finding nearly double the number of significant markers. Is this expected behavior?

runCalc:
myGAPIT <- GAPIT(
Y = myY,
G = myG,
#CV = myCV,
#KI = myKI,
kinship.algorithm = "VanRaden",
PCA.total = 3,
kinship.cluster = "average",
kinship.group = "Mean",
model = "CMLM"
)

runKin:
myKI <- read.csv("Genotype.Kin_VanRaden.csv", head = FALSE) # from runCalc

myGAPIT <- GAPIT(
Y = myY,
G = myG,
#CV = myCV,
KI = myKI,
#kinship.algorithm = "VanRaden",
#PCA.total = 3,
#kinship.cluster = "average",
#kinship.group = "Mean",
model = "CMLM"
)

[Lightoscope]

I reran runKin, and runKin2 results are identical to runKin results.