to be honest I am not sure, the best would be: send subtitle on opensubtitles.com (link) and what you try to search - with language setting. Then I can forward this to developer so he can look at it - we need to replicate problem first in order to fix it. So please be descriptive.
for this upload case, you can contact me directly and we will find the solution. I believe there is also already some commandline tools which can do that...but anyway, write me PM/email.
hm, getting it via name is a bit problematic. If you would write me if it is with all episodes in season 2 uploaded by SubsceneImport and all episodes are shifted by 1, so I can make some magic maybe. So all subs from 2nd episodes should be -1 episode only for season 2 right ?