Could it be that, what you are detecting is early apoptosis and DNA fragmentation has not occured yet?
Also note that caspase-3 activation does not always herald death through apoptosis (check 2 examples in the link and file provided), hence othen markers can also be used such as annexin-V labeling.
Sure. Depending on the stage of apoptosis or maybe the kind of cell death you may see different results. Better indications fpor apoptosis are Bcl-2/Bax ratio determination (RT-PCR), caspase activation (mostly 3 and 9 maybe via Wb od an assay), Cytochrom c release (Kit via WB) and the silver standard is FACS determination via AV/PI staining.