Hi the matrix coordinates entered do not match the drawn one 

library(flowCore)
library(flowViz)

library(flowStats)
library(flowClust)
library(parallel)

x <- read.FCS("PD03 Net 23122016.fcs", transformation="linearize", which.lines=NULL,
         alter.names=FALSE, column.pattern=NULL, invert.pattern = FALSE,
         decades=0, ncdf = FALSE, min.limit=NULL, dataset=NULL, emptyValue=TRUE)

Xtrans <- transform(x, transformList(c("SSC-Log_Height", "FSC-Log_Height", "FL1-Log_Height", "FL2-Log_Height", "FL3-Log_Height", "FL4-Log_Height", "FL5-Log_Height", "FL6-Log_Height", "FL7-Log_Height", "FL8-Log_Height", "FL9-Log_Height", "FL10-Log_Height", "FL11-Log_Height"), log10))

Chaeto <- matrix(c(1.5,2,2.5,3.2,3.3,3,1,1.8,2.2,2.5,2.2,1.5),ncol=2,nrow=6)

colnames(Zoox) <- c("FL4-Log_Height","FL2-Log_Height")
pg <- polygonGate(filterId="Counts", .gate = Zoox)
pg

Polygondata <- Subset(Xtrans, pg)

xyplot(`FL4-Log_Height` ~ `FL2-Log_Height`, data = Xtrans, filter = pg, smooth = FALSE, bin = 256, stat = TRUE, pos = 0.5, abs = TRUE, outline=TRUE)

The polygon doesn't match the selected coordinates: http://imgur.com/qHFt5ul