This is perplex but interesting problem--yet the answer to it is fairly straightforward to trouble-shoot. A florometer is a very simple instrument consisting of a light source, a wavelength specific filter, a detector (measuring meter), and a LED display to show the data. From what your blogging it appears that the problem is not the light source, not the filters, and not the LED display; therefore, this leaves only the Detector.
What florohore are you using in the experiments? And, what are its spectral characteristics (excitation & emission waves)?
Hopefully, the other chrom writers can add some explanation to your quandry.