Hi,
Thanks for the feedback and the bug report, I have saved a copy of your post and will look into these things.
Yes the size of a tile-set is currently limited to 65536 and a char-set is limited to 500,000, allowing more tiles would be simple enough, although the CTM project file format only supports 16-bit values (max 65536) for both chars and tiles, so you would still need to reduce the count before a project could be saved.
Was the bug you found seen when doing a binary file import of map data?
Anyway, I will try and look into these things before the next release.
Cheers!