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View>Smart Guides are your friends; if you drag one by the Anchor Point, they will say anchor point when you are there, on top of the other.
It may also have something to do with Align to Pixel Grid, if you have it turned on; you can see that in the Transform panel.
Apart from that, you should have a look at Edit>Preferences>General>Keyboard Increment, which determines the nudging steps.
Unfortunately the problem persists. If I zoom in, I can move objects around in very small steps with the cursor. However, the cursor is not very sensitive and it can become mind-numbingly difficult to get something EXACTLY where you want it with the cursor, thus the use of nudging. Nudging at this level, even with the increment set to the smallest measurement possible, still sends objects much further in any particular direction (like, 5 - 10 pixels-worth) than does the cursor, basically defeating the purpose.
VERY frustrating. I have one program that has pixel-perfect accuracy but only creates rasters, and another that will create vectors but has the accuracy of a drunk Boieng 747.
What happens if you use Smart Guides? Does it work or jump away?
I am afraid there is a host of snapping options.
You may try to look into the Helpfile and search for Snap.
Maybe someone with a newer version will give some suggestions.
Can't really help, but I'm having this exact problem. I'm using CS 6, and I can't seem to find the "Align to Pixel Grid" option. Adjusting the nudge distance in preferences doesn't help either (I have it set to 0.0002, and its moving 1/16" when I nudge).
Try the Transform panel. It's only on by default if you use one of the Web presets for your document setup but it can be on for individual objects even if you copy them to a new, clean document.
I know this is an old post but I have been having the same problem on my PC using CS6.
For anyone with the same problem try saving your files and closing Illustrator.
Then hold Shift+Ctrl+Alt while relaunching the program and allow the changes to reset any of your previous custom preferences.
Worked for me.