The English SUP subtitle files that QTS included with their batch torrent for Gundam SEED HD Remaster were taken directly from the blurays and as such have an internal resolution of 1920x1080. QTS's encodes, however, were 1280x720. As such the subtitles either appear off-screen or are not loaded at all (if your player does a resolution sanity check).
I have corrected all of the subtitle files to have an internal resolution of 1280x720 so they should work properly now.
2/15/2013 Edit: Thanks to Bronx01 for bringing up that the subs for episode 49 did not work. It turns out that QTS ripped them improperly and they were coded to start a second after the episode had ended (!). I have re-timed the subs to work properly and the v2 can be downloaded here:
http://www.sendspace.com/file/05rtxy
My apologies for the inconvenience.
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