I found a work around, however, it may not be for everyone.
Using the free program, Subler, I did the following -
1) Opened both the HD and SD version in Subler
2) Delete ALL the subtitle tracks in both the HD and SD files. (Note: I've tried deleting ONLY the English track, as that seems to be the one that iTunes is automatically pulling in, but when I did that, it actually automatically pulled in the Spanish track, so it seems deleting all is the only way)
3) Save
4) Delete the file from your iTunes library, (but obviously keep the files) then reload.
Wham bam. Thank you ma'am.