My lab has a long tradition with apoptosis, TUNEL and ISNT (see for instance
Gold R, Schmied M, Rothe G, Zischler H, Breitschopf H, Wekerle H, Lassmann H.
Detection of DNA fragmentation in apoptosis: application of in situ nick translation to cell culture systems and tissue sections. J Histochem Cytochem. 1993 Jul;41(7):1023-30 or my latest publication; Bauer J, Elger CE, Hans VH, Schramm J, Urbach H, Lassmann H, Bien CG. Astrocytes are a specific immunological target in Rasmussen's encephalitis. Ann Neurol. 2007 Jul;62(1):67-80.).
I think that if you have "weird" results with your kit, you probably will have the same problems when doing ISNT. During the last years we have been using the Roche kit and I think it is working excellent. Note however that both ISNT as well as TUNEL cannot discriminate between apoptosis and necrosis. Therefore, if you want to look at apoptosis, I would in addition use an activated caspase-3 staining. If you do both, you may find that they will may not have the same staining pattern, one of them may stain more, the other less because they label apoptotic cells at different stages of the apoptotic pathway. Maybe if you tell us what you mean with weird results we can help you in solving your problems. It may also happen that your TUNEL is positive and your caspase-3 negative. This means that your cells either are necrotic, or they follow a non-caspase mediated apoptotic pathway