I am running VLC 2.0.3 on Windows 7 and certain episodes of a show have very large subtitles. I tried changing the "Font size in pixels" option in the advanced settings under text renderer, but that didn't change the subtitles themselves. I did noticed it changed the size of the text for the file name splash for when the "show media title on video start" under normal options in Subtitles & OSD. I have deleted the %appdata%\vlc folder, tried the nightly and tried older version 1.1.11, but they all have the same issue. I have used MKVExtract to get the subtitle files from one video with the issue and one video without the issue that are both part of the same show and the only difference was the good subtitle had "Video Zoom: 6" and "Video Position: 0" while the bad had "Video Zoom: 5" with no video position. I changed it on the bad video to 6 and added the video position then added that sub to the file using MKVMerge, but the video still had very large subtitles.
If I open the file using MPC-HC the subtitles appear normal.