Acacia and dark oak not identifiable by Mineways currently. Pots made in 1.7 will not have any contents, as they rely on tile entities for the contents, not supported by Mineways.
I really should bite the bullet and figure out tile entities, e.g. http://bedrockminer.jimdo.com/modding-tutorials/advanced-modding/tile-entities/
Might be useful to update the documentation page to make it 1.7 and later, as well as remove the contents removed entirely on any levels made after 1.6.4 if possible, since they appear to display differently on newer versions of Minecraft from how Mineways renders them (I couldn't find any correlation with their legacy tags, but I'm not 100% sure.)
Updated the docs (visible in the next release). I believe flower pots made in 1.7 and later will always be shown as empty. By the way, how did you generate those pictures? That is, is the test world you have there available for download, or can you send it to me? Looks handy for testing. I have a similar test world (it's built in to every version of Mineways, "[Block Test World]"), but it's a bit sparse.
Debug mode. Everything was generated in 1.10, but debug mode is a little weird, and it might be that blocks like that wouldn't ever actually be created.
Wow, and thanks - a fascinating place is Debug world, and with two little commented-out assert() statements Mineways can export it. I just need to add redstone wire and tripwire hook export and I'll have the new version done...
The good news is that today I discovered that Minecraft has (finally) added a way to tell what version Minecraft world the file is: the Version ID is greater than zero when the world is 1.9 or newer. So I've turned everything into empty flower pots if the version is 1.9 or newer. This will be in version 5.01.
Awesome, can't wait!
Partial fix is in V5.01, i.e., all pots are now empty.
I've added code that now reads Block Entities (boy was that a pain), stores this additional data away, and uses it when reading the world for export. This addition also turned up a bug fix, that acacia and dark oak saplings were not exporting properly. Long and short: flower pots are now filled. This fix will be in version 5.04.
Indeed fixed in Version 5.04 and ready for download. Along the way I fixed the cactus' material (it was not assigned properly).