I have been able to solve my own question... with the help of this site:
Form 1099-B TXF Reference Numbers
The .txf file that was exported through TokenTax had a bug and was created with incorrect holding period reference numbers.
The bug was reported to TokenTax and has been resolved. .txf files generated now have accurate reference numbers and are imported into TokenTax Desktop on the correct lines on Schedule D and form 8949 is generated appropriately.
If anyone wishes to interpret a .txf file (easy to open via a txt viewer) the site linked above is a great reference tool.
