blessedk, I think you just have to reselect the cursor tool in the graph palette after you zoom in to get the cursor back. The cursor changes with the graph tool you have selected, so that is what it sounds like if I am understanding you correctly. Hopefully that helps!
If you are interested, I've built and will be presenting at a future user group meeting, some nice graph extensions for this sort of thing to be improved in LabVIEW. You can check out the open source project here.
Cursor work by locking to points on the graph, so if you zoom in where the cursor is out of view, you won't be able to still drag that cursor. in the cursor palette, you can right click to bring a cursor to center, which would let you grab it, but sounds like you are fighting how cursors work, which I'd really recommend the graph extensions to replace them, since they are way easier to use and look better as well.