Here's something to try. BUT FIRST: make a backup copy of your TXT file and keep it out of calibre. (This is just to play it safe and can be deleted if these instructions work for you.)
1. Convert TXT to TXT with "Remove spacing between paragraphs" selected.
2. On the "Remove Books" icon, use the down arrow to select "Remove files of a specific format" and delete "Original_TXT".
3. Convert TXT to MOBI.
This has worked for me ...