Any time I have seen a route discontinuity (they're not uncommon when you're programming your FMC) that means there is an actual disconnect somewhere. You know about setting the view to PLAN and stepping through your flight plan on the LEGS page? Once you find the disco, click on the waypoint below it to copy it into the scratchpad, then click on the disco to close it up.
It helps to know what is going on behind the scenes when you are programming your FMC. For instance, when you say you are putting in a route, are you using the "via-to" method and inputing airways on the route page, or doing them all direct on the route page, or adding them on the legs page directly?
Keep in mind that outside routes may be produced with different AIRACs. Have you downloaded and installed the latest from Navigraph? If you want up-to-date navdata and procedures, many manufacturers require this; Navigraph charges a small fee for this service (one of several they offer).
It is your responsibility as pilot to make sure your route makes sense and there are no problems. Are you downloading your airport diagrams for taxiing, your SIDs and your STARs and runway approaches and comparing them to your FMC data?
I sometimes have to tinker with routes until I am satisfied with them. Usually. There is a learning curve to this. People think the 757 Captain is just a pretty bit of fluff. Wrong. The FMC is complicated.
Jim's approach is a good one. He's working with the system, trying to figure things out. That's what it takes.
I'll just tell you quickly (I need to get back to work) how I do it.
I program the FMC on the route page using airways, like UM221 on the left "via" side to wherever I am getting off that airway, which will be a fix, like SEXXY. All the waypoints along that route are entered automatically, and I can see them on the LEG page. When I know what runway I'm taking off from, I'll put in the SID (finding the right one for my route by looking on SIDs I get from AirNav or someplace). There may be some duplication, so I go through and delete and mess with until it all looks right to me. Sometimes it is all perfect right from the start; sometimes I have to tinker.
If you have a good idea what runway you are going to land on, put that in, too, and the STAR. Again, I go through the same process as for the SID. As I mentioned earlier, sometimes they will leave you hanging for ATC, sometimes they will roll out the red carpet for you right to the runway threshhold.
Ideally, you should have your STAR showing on your PLN display in front of you, with your runway and missed approach already put in. The MAP will usually look like a racetrack somewhere off the to side of the airport.
Make sure your altitude constraints match up with your published documents, and don't consider yourself finished until you know your route is correct, have fixed any discos, etc. etc.
Now, let's say your cruise is 30,000 feet, Jim. You are going to get something less than that from ATC when you get clearance, say 6000 feet. That's what you set your altitude to. VNAV will take you up that far and hold, switching to SPEED. When you are cleared to go higher, dial it in and hit VNAV. Now you ascend to that altitude according to your original profile. Keep doing this until you are cleared to your final cruising altitude.
Coming down, I usually don't use VNAV with ATC. I like Flight Level change instead. Usually, all bets are off anyway, as ATC is going to vector you around. HOWEVER, if you want to do without ATC, dial in a low altitude before you reach your Top of Descent. VNAV will automagically head down on schedule and follow your plan / vertical profile.
I think some of the problems are that people are (understandably) learning about this airplane. Yeah, I've had (I'll go ahead and say "other") Airbusses, 737, Ejets, MD-11, Queen of the Skies, yadda, yadda, yadda But while I consider myself ahead of the game on learning this one, this is the firsts FMC that has inspired me to really learn how to use the darn thing.
EDIT: ha, I can write darn and it looks like darn. Anyway, here's another tip.
To learn this bird, just forget ATC and turn off traffic. Learn how the FMC controls your flight using maximum automation. I always make that call before I do anything: ATC or not? I have Radar Contact, which is much, much better and will leave you alone to do your published procedures, but even so, if I want to sit back and watch Robo-Plane work, I will not use ATC. Period. But keep in mind, this is not an Airbus. Pilots are not optional!
On the other hand, if I want to fly "realistically," there is no way I am having VNAV get within ten feet of my descent. I am going to be responding to controllers who don't give a crap about what I've programmed into my FMC. DO NOT USE VNAV FOR DESCENT WITH ATC. In the final stage I'm using V/S and manually setting speeds. Read your manuals, friends.
I honestly believe that if you if follow my advice here, you'll get more out of your airplane, unless your install is FUBAR, which can happen, too. But believe me. The FMC works. I has yet to fail me when I have done things right on four flights in two hemispheres.
ONE MORE darn THING:
Once you get your route the way you like it, be sure to save it as a company route. That way you don't have to mess with it next time. One of the really nice features of this airplane is that y ou have so many options. Also, don't forget you can program your Route 2. I have actuallyl started doing that, too.
Again, if you want pre-made routes I know work, download that 100 World's busiest. Try those out, and I bet you'll see how well this thing works.
Written in haste and rambling, sorry.