Oh no. The first version is on github if you want to revert until I have a chance to fix this. In .9.1, against my better judgment I replaced Alfred's standard way of selecting files with a home-brew version. This was so that it showed the full list of files before you start typing. A side effect of this is that it is not aware of Alfred's search scope (which is not great) so your guess that this is the issue would not have helped. More so it doesn't seem to work for everyone!
Would you try this command from Apple's Terminal app and see if it finds your TP documents please:
mdfind "kMDItemContentType == 'com.taskpaper.text'"
If it doesn't find what your are looking for could you try:
mdls -name kMDItemContentTypeTree [path_to_tp_doc]
on a one of your TP docs and report back what it shows.
At this point though my inclination is to revert back to Alfred's standard approach and improve the subtitle to avoid the confusion that it caused.