Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocalLooking at the excitation and emission curves for DAPI and Cy3 I suspect
bleedthrough.
Using exactly the same excitation protocol you use for dual DAPI/Cy3
imaging,image DAPI and Cy3 only labelled cells to determine if
bleedthrough is occurring.