This has been fixed in v1.0.9, which I opted not to release on vBulletin.org due to other issues that cropped up as a result of that fix.
v1.0.10 will be available tomorrow and will fix this issue along with all other reported bugs in v1.0.9. If you want, you can download v1.0.9 from our site just now, which will enable your forums to work with the stopwords filter turned on globally.
Thank you for your patience, and sorry for the inconvenience
Fillip