Well, I figured out the problem was that I had already surveyed those bodies. There is a check box on Display2, or Minerals; one of the tabs on the F3 menu. Anyways, it reads "Show Surveyed" or something like that, and it solved my issues.
I've been rolling with Commercial Survey Ships for a Geo Survey-only craft, and a Military ship for a Geo + Grav Survey craft when I want to use both. I use the Conditional Commands set to "When at 50% Fuel" / "Refuel at Colony" for my Commercial Ships, and add "When at 50% Fuel" / "Begin Overhaul" on my Military Ships, since Overhaul takes awhile it let's the crew go on shore leave and refills the morale... and resets the maintenance clock, too.
I use the orders, "Survey nearest Planet or Moon" and then have "Survey Nearest Body" as the secondary order. I manage Jump Point Surveys manually, along with Jumps. I go to survey points three at a time, before refueling, and six at a time before Overhaul. It's a pain, but when I find a Jump Point, I manually jump through it, then RTB and continue surveying. Lather, rinse and repeat until no unsurveyed Jump Survey Locations exist. You can use the "Exclude Surveyed Locations" check box in the Orders Menu to make manually ordering the Jump Point Surveys far easier.
I set up a forward Orbital Habitat w/ Maintenance Modules before conducting surveys in a new system, usually with a dedicated Jump-Capable Carrier, using hangars and parasites to conduct the actual Geo Surveys. Tonnage wise, it's cheaper not to use hangars, but a 2x Hangar or 4x Hangar Ship with enough berths for it's flight crews and 20 persons worth of Survey Teams (one for each, Geo, Xeno, Diplo, Spy), makes a nice carrier later on. And thus far I've found Fighters are easier to upgrade than larger ships. Plus the Carrier can serve in other ways when Geo Surveys aren't needed.