Could be one of a few things causing that... can't say really.
Let me repost a thread made by Skuzzy a long time ago, but it still holds true, about building new terrains:
Originally posted by Skuzzy
Ok, here is a rough/broad list of tips to help keep terrain building trouble free.
1) Get all your elevations and tiles laid into the terrain. Elevations are important to get right early. If you change an elevation, you will need to rebuild the road system or find the roads effected by elevation changes, delete them, and manually add them back.
You cannot have a zone master in zones 1, 2, or 3. These zones are special and must contain the HQ for each country. Field 1 must be Bishop and must be in Zone 1.
Now hit the "Water not 0" button in the terrains tab. Fix any of these. Important to do as this will involve altering the elevation.
2) Next, lay in your field/towns/objects. Note: Make sure you set the elevation of objects to the same, if they share any vertex points int the terrain. This especially true for fields sharing any vertex points in the terrain.
3) Now, run the "Obj. Report" in the "Objects" tab. NOTE: You no longer have to close this window as long as you do not delete an object. Correct any errors that pop up.
4) Now, go to the "Roads" tab and hit the "Create All" button. This will lay in all the roads/convoys/tracks/trains for your terrain, running from South to North. You can and will need to move them around after this.
5) Repeat #3 and fix any problems. At this point the only issues you may have will occur when a starting or ending point of a road is too close to another object.
6) Now, lay in your task groups and all your spawn points. Be sure to set a waypoint for each task group. The CV in each task group must be the first ship in the list.
7) Now, run the "Check Entry" in the "Objects" tab. This button will check all your spawn points for correctness, visually showing you each one it is checking. It will stop on any offending spawn point. If it does, then fix the spawn point, and hit the button again.
Repeat until you get the "Checking Complete" dialog box.
8) Now run #3 again. Fix any errors.
9) Now would be a good time to hit the "Redo" button in the "Roads" tab. You can hit this anytime you like. What it does is put all the convoys/trains at the correct starting point and sets thier end point.
If you change elevations, you have to do this again. If you move a road, you have to do this again.
Do not attempt to manually add the convoys/trains to the terrain. You will make a mistake doing this and this will be a source of some bizarre side-effects.
10) Now you can setup your fields. Just be concerned about getting the country assignments done. Once done, hit the "Standard" button and it will correctly setup the planes, boats, vehicles, and so on, for each field.
Then make any custom changes you want.
NOTES:
a) Do not rotate the ships. Leave them at thier default orientation.
Detail wise, there are many things to be concerned about, but the above design flow should help reduce the effort in getting terrains completed and pretty error free.
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Notice how many times he says to rebuild the roads, or redo objects... this can be a very critical thing for properly-working strat.