So there are a few things you can do. First, re-do your calibrations since you mentioned they are suspect. If you're over-extruding, you'll see your bed shake from the nozzle clobbing into already-laid filament, although this certainly isn't a guarantee. It's good to check and re-calibrate this every so often with a cube.
Second, print in layer heights that are a multiple of your Z-rod thread size--search the forums for "2963," there is a ton of information. I don't know what kind of Z rod is on the Da Vinci. This should prevent your nozzle from dragging along the top because your Z rod will not be trying to make movements not possible due to the thread depth. On Solidoodles, they use an SAE 5/16 inch - 18 rod, and 0.2963 mm comes from that--it's the closest to 0.3mm.
Third, try using the Z-lift settings in slic3r only if the above two things don't help. Z-lift will likely stop this entirely, but it's slowwww. Just depends on if that's worth it to you or not.
Fourth, I'd recommend upgrading the hotend to an e3d. No matter what, the stock hotend on my solidoodle always created rough finishes. I haven't had a rough finish with the e3d yet, no matter how crappy my settings are. You can't expect great results without a great hotend, so keep that in mind.
I hope this is helpful.
n2ri wrote:this topic is about holes in flat tops I know but every time I say anything about settings I use for my printing and why. Wardjr always says the same line. like I dont know what Im talking about but he does yet havnt seen pics of it yet. Im an ol 'show me' boy. and I have done lots these prints and tossed many due to not using the settings I do. also sometimes support messes up part way into a print and has spots without support by the time top goes on, either due to support settings, print shapes or just odd errors during print.
I don't want to prevent the OP from getting help because of this nonsense but all of the things you describe are symptoms of a poorly calibrated machine. You might want to consider that you actually have no idea what you're talking about. Please do not speak with such authority, it is detrimental to those who want good results from their machines. "Random errors" are not something you should accept from your printer, if your time is valuable. I debated just ignoring you, but I want the OP to know that your advice is greatly misleading.