I performed Homer's annotatePeaks.pl on multiple tissues, yet when I run annotatePeaks on the merged tissues, I get fewer total annotated peaks. Is there an explanation for this?

Question

[Ronin]

Let's say I have run Homer's "annotatePeaks.pl" on multiple tissues (eye, liver, spleen), and get, lets say, X, Y, and Z total annotated genes/regions, where X, Y, and Z are just different numbers. My thought was that if I merged the peak files from these tissues (mergePeaks.pl) and run annotatePeaks.pl on that combined set, I would get X+Y+Z total annotated genes/regions, but I do not see this.

My reasoning here has to be incorrect, yet I do not know why for sure. I would appreciate any insights as to why I find this difference.

edited for readability