Batch effect that is same as main factor

Hi all,

I have RNA-seq data of 54 samples from 6 mouse brain regions with 3 different groups.
One group is control (no stress), another group is stress-resilient (Res) and the other group is stress-susceptible (Sus).
These 54 samples are sequenced in 5 different days. (day of library prep. is different)
Most of the data with the same brain region are sequenced at the same day.
So I tried to perform batch correction using ComBat, but it seems that the difference by region was normalized.

In this case, any suggestion?

This is my ComBat R script:

datexpr <- read.csv("FPKM.csv", row.names=1)
trait <- read.csv("trait.csv")
trait$seqdate<-as.factor(trait$seqdate)
batch <- trait$seqdate

datExpr.combat = ComBat(dat=as.matrix(datexpr), batch=batch, mod=NULL)
write.csv(datExpr.combat, "Corrected_FPKM.csv")

And My data information (total 54 samples):

    Region State Seqdate
1    AMY   Con   191214   x 3 (ex. AMY_Con1, AMY_Con2, AMY_Con3, same below)
2    AMY   Res   191214
3    AMY   Sus   191214
4    HIP   Con   191214
5    HIP   Res   191214
6    HIP   Sus   191214
7    CBC   Con   190826
8    CBC   Res   190826
9    CBC   Sus   190826
10   NAc   Con   191029
11   NAc   Res   191029
12   NAc   Sus   191029
13   PFC   Con   200317
14   PFC   Res   200317
15   PFC   Sus   200317
16   VTA   Con   200427
17   VTA   Res   200427
18   VTA   Sus   200427

Refer to the following question.
Batch correction using DESeq2

Thank you!