Issues with cuffdiff

[ClemBuntu]

Hello,

I'm performing an analysis containing 3 samples per conditions and 5 conditions (so 15 samples in total). I want to do pairwise comparison for each condition.

I'm just starting using cuffdiff.
Firsly I just tested cuffdiff with only 2 conditions, like that :

cuffdiff -L control,A -p 16 --library-type fr-firststrand --no-update-check  reference.gtf control_1.bam,control_2.bam,control_3.bam A_1.bam,A_2.bam,A_3.bam

And I obtained 3 differentially expressed genes in the gene_exp.diff file.

Then I tried to do all my comparisons in one command line :

cuffdiff --output-dir allComparisons  -L control,A,B,C,D -p 16 --library-type fr-firststrand --no-update-check  reference.gtf control_1.bam,control_2.bam,control_3.bam A_1.bam,A_2.bam,A_3.bam B_1.bam,B_2.bam,B_3.bam C_1.bam,C_2.bam,C_3.bam D_1.bam,D_2.bam,D_3.bam

And looking at the gene_exp.diff file in output, I obtained 2 differentially expressed genes between control and A which only one in common with the 3 genes I obtained before.

Which analysis I should trust ?
And what is the good way to use cuffdiff ?