What causes this?

Well, I am sure my suggestion is going to fall on deaf ears as my humble opinion, if you can afford it, I would buy a mini-mill. Mills are more precise and accurate with the X-Y table. However, regardless, your vise and drill should be squared up (that is if you are using an X-Y) table.
 
I have a mill but unfortunately it is a mill lathe combo that I was using as my thickness sander. One of the problems with using one machine to do multiple functions. You spend more time swapping back and forth so you wind up doing jobs with a less than optimum machine. I think I made the ribs a little small so I might be re-doing this. I will use the mill next time.
 
the very thin bit drifts with the wood grain. to do it better... use a very slow feed and a short drill showing in your chuck to keep it stiffer and straighter.
 
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Another method drilling straight into a wood is using end mills in drilling press instead of HSS drill bits. HSS is very flexible and may wander sideways. Take mill out of the hole often getting deeper little by little.

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Tried this today. Worked slick. Holes are dead straight. Didn't break any mills either. Well, yet ;)
 
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