Meshes appear in Map Maker, yet not in-game.
I cannot tell for certain 100% if this is the case, but it honestly sounds like a standard mix-up on your side where you have your exported map in cape, if you have several different exports of the map, and whether or not the new export when through correctly, many people make this mistake and in all honesty, if the objects show in the map maker, it should not be many reasons why it shouldn't show in the exported map in the same FH game folder.
You might know this already but I will mention it any way, keep in mind that if you ever exported the map at an earlier stage and it's still inside of the exports folder it will also show in cape along with the map itself in the map maker that has "has portal" marked(you'd pretty much have 2 versions of the same map). Another thing to point out is that if you diddled around with the map a lot but have two different mapnames with the same display name, only display name would show in cape and you'd more than likely enter the wrong map since you cannot know for certain which portal to enter. With other words, make sure you do not have any extra copies of your map in the exports folder.
If the map maker can see the objects, there's not much reason why it wouldn't work when you go into cape and through a portal there, it loads the map from your game the same way as far as I know, the only difference is that it also starts a process on our FeralHeart server and lets you use your character and be online.
The only other reason why objects wouldn't show from cape, while it would from the map maker would be object conflicts of some sort with object groups having objects with the same names but no actual objects bound to them but I do not quite see how that would work. Most of the cases it's really down to wrong map portals walked into in cape, too many copies of the map already or just a general mix-up or clutter.
Of course, as mentioned above, keeping structure in your own object groups and NOT taking use of the standard ones like MyRocks, MyTrees etc, can be handy. No one should really use the default groups for custom meshes.