I thought I'd try to help you address your issue, but I'm afraid that much of what I have to tell you won't exactly be welcome news... So, the good news first! It IS possible to make a map as you describe it. I have made custom maps (and edited premade maps) with fixed starting points. The bad news, as you have already surmised is... the Cartographer's Table tool is extraordinarily buggy.
So, onward to the actual trying to help!
Having played with the Cartographer's Table, I can tell you the most important thing I learned: you must exit the game completely, and restart the game, and only then can you reload your work to be able to see any changes you have made. Yes, I know, that's crazy, but in my experience it was true.
It's buggy. That's the key thing to know going into it. It became more apparent to me why they wanted to charge more for the map pack once I saw how time consuming the tool was. Using the Civ 5 World Editor, you could crank out the equivalent tp the DLC Map Pack in an afternoon, but I'm sure it took them a while with the tool they are using. No, I don't know why they didn't fix the tool's bugs first.
You will also see maps that started off as "Large" suddenly appear marked as size "Tiny". This happens when you trust that "overwrite file" button when you want to save your (updated) work. Save your updated map changes as a new file name. Later you can go into C:\Users\Username\My documents\My games\fallen enchantress\data\maps and delete all the old versions and thumbnails once your work is finalized. Obviously, when working with a buggy tool, multiple save files are time saved later if things get messed up somewhere along the way. It's worth the extra file names and the work to delete them when you're done.
The Cartographer's Tool is like a skittish horse, it can get you from A to B if you're patient, but it is not to be trusted implicitly. Compared to Civ 5's or even AoW:SM's map tools it is still in the toddler stage of development.
However, many people are saying that they wish that fixed starts were added to some of the Map Pack maps and I found that to be a pretty quick and simple fix saved as a new map name, something creative like "Anythys Fixedstart Tarth". (Remember you will be player 1).
If you google search for "Fallen Enchantress Cartographer's Tool bugs" you'll see what I mean about the limitations of the tool, but the ability to change and create maps with difficulty is certainly preferable to not having any way to do it at all.
It's very likely that you tried to overwrite an edited map name, or tried to load your work without exiting the game completely and restarting first. Give it another try, making changes in small increments and saving (new file names) as you go. Hopefully these suggestions will help you navigate the tool to let you experiment with different map configurations and starting conditions. It's a genuinely difficult tool to work with, but it CAN do some of the things you are looking to accomplish, if you know some of the quirks.
Best of luck!
P.S. Thankfully, the game itself is in a more finished state than the Cartographer's Tool. It has bugs as well, but nothing to the extent of the limited functionality of the Cartographer's Tool.