Lower sensitivity in NIR range is expected, because excitation lamps often have lower emission in NIR range, and detectors are often orders of magnitude less sensitive in NIR.

According to the spectrum of UV excitation lamp of Agilent FLD you can see low intensity in NIR range corresponding to your excitation wavelength. Agilent does not provide spectral sensitivity function for their detector in this document, but please find below a curve for R928 PMT often used as a detector in cuvette fluorometers and well plate readers:

Typical spectral response for R928 PMT 

Typical spectral response for R928 PMT 

As you can see, it is about 1.5 orders of magnitude less sensitive at around 800 nm than at optimal wavelengths around 500 nm. NIR dyes have also somewhat lower quantum efficiencies than visible range dyes. These all factors are multiplied to give 100-1000 fold lower signal in NIR when detected using most conventional instrumentation.

Lamp energy distribution

 Lamp energy distribution

Therefore, we recommend to perform optimizations to improve sensitivity (use broader slits, and perform spectral scans to ensure you are operating at maxima of excitation and emission spectra). Signal intensities for NIR dyes and visible range dyes are not directly comparable.