I finally got around to playing with nuclear engines. Meh. Not as good as I thought. Using the same overall design from before, only changing the Rockomax Poodle engines out for the nukes, a trip to and back from the Mun ends with pretty much the same fuel situation: I'm out and I'm using reaction thrusters to push my periapsis that last few meters into the atmosphere to let drag take care of the rest. I suppose the main advantage to the LV-N is that it only uses Liquid Fuel and no Oxidizer, making it good for spaceplanes, or easier refueling stations.
Also, why the hell is it easier to make a round trip to Minmus than Mun? The Poodle-based craft from before makes it to and from Minmus with a good amount of fuel left, but not Mun.
Are you landing on Minmus or just doing a flyby? If you are landing then it is because it takes a lot less fuel to safely land and then take off, and this outweighs the extra fuel needed to get there. Now, depending on how you set up your flybys, it could be that you are doing everything very inefficiently for the Mun while doing it efficiently for Minmus. I don't know how to really explain it very well, but you need to remember to look at your orbit after your flyby, along with how you exit from the planet and which way the planet is rotating. Lets say you are just doing a flyby of the Mun, without establishing an orbit. Most of the time, you will get a rougly circular orbit of Kerbin afterwards. This is very, very bad, as you will waste most of your fuel trying to lower your periapses. Instead, play around with the manuever node until you have a highly elliptical orbit with a periapses hitting Kerbin, or only a few hundred kilometers away. While you will be hitting the atmosphere at a higher speed, you can use whatever fuel you have saved to slow down, and then absorb the rest on your heat shields. If you land, look at what direction whatever moon you are on is orbiting compared to Kerbin. Generally, to use less fuel, you want to have your escape vector in the opposite direction, since this will lower your speed. Again, play around with the maneuver nodes to found out which gets your periapsis the closest. If possible, always try to take off in the direction the planet is rotating. This gives you an extra boost from the planet or moon, and is the main reason you head east from the space center every time.
Not sure how good of a player you are, so sorry if you already know most of this, but those are the main reasons I can think of for why you might have discrepancies getting from one place to another. Now, onto the nuclear engines. Mainly, you want to be using them for transfers. When landing, they are inconvenient because of both their size and their low thrust. It has approximately the same thrusts as that other 1.5m LV engine, can't remember the name at the moment, but has more weight. If you just switched it out for a poodle, make sure you don't have any oxidizer in the fuel tank, and if possibly try to use the airplane parts. A well designed stage with the LV-N can get you from one planet to another with ease, but if your craft is to big it will take forever. Generally, LV-Ns kind of act like ion engines, where you have very effecient ISP but low thrust to weight ratio.