I don't know.
Are you sure your "housekeeping" gene used to normalize the qPCR is not regulated in this experiment?
The PCR is for certain primer sequences located in one part of the gene. One possibility is that there are alternately spliced transcriopts of the gene produced. there could be more total transcript, but less protein producing transcript produced in treated groupd, or less protein that binds the antibody used in the ELISA. For example, an alternate splice may have a different promoter giving it different tissue specific expression, or an alternate exon may be omitted from one transcript that is the location a monoclonal antibody binds to.
There could also be regulation at the translation level, by non coding RNA for example, or by an RNA binding protein. There could be factors affecting RNA stability.
The primers could PCR mRNA, but they may also PCR non coding RNA. For example an antisense RNA upregulated in treated tissue could increase RNA /PCR product level, but might inhibit protein expression. (Don't ask me how common that is).