Which kind of matermix you are using?

Ct value is the interpolated cycle where the sample crosses an arbitrarily defined fluorescent threshold value. It is (relatively) representative of the concentration of the starting material, but onto itself not a measure for DNA quantity. If you set the fluorescence threshold low, the samples will cross that threshold at a low Ct.

Have a look at your amplification curves to see if it plateaus at your final cycle (35, 40, 45). A plateau would indicate that no further amplification is occurring. If plateaus do occur in the wells that you are pipetting onto gel, you could combine several wells of the same amplicon to get a stronger signal on gel. You can also increase the amount of DNA dye in your gel. We use 1/20.000 midori green to visualise DNA, but for dificult to see amplicons you could choose to increase this to 1/10.000. Good luck