How are you centering your spindle over the markings?
Its all very well having the debate of spot v centre drills (and I use both, but favour centre drills simply because I have several and they are cheap to replace), but the iisue seem to me to be that you are eyeballing the drill tip to the marking... before using a centre drill you still need to get the spindle accurately centred over where the hole needs to be... and for that you need a wiggler, or an edge finder if you can locate the hole relative to two perpendicular edges... unless of course you are relying on a DRO but then you wouldnt really need a mark, you'd just dial in the location...
If you're in Europe why not come and visit the UK CNC Community at http://www.mycncuk.com