I had problems with a patchy Hoechst stain, but I redid the staining with the inclusion of 0.01% triton X-100. The results were great, maybe this can help you.

Thanks Jurgen, I'll try that.

Triton is good at permeabilising cells allowing the nuclear label to enter the cells. However, sometimes certain cells tend to wash of and if this is the case another permeabilising reagent such as methanol or acetone can be used.

You can also try not rinsing the DAPI. We regularly use DAPI in the coverslipping medium and it works great for our tissue.