I have never had that experience. But, in VLC, go in the Video menu and the last item is subtitles track. You can try to turn them off there.
I'm using MeGUI to overlay my subtitles on mkv videos (that also have embedded default subtitles).
I read the video source with DirectShowSource command, then TextSub my srt file on the video.
The problem is that the output video has two subtitles, mine over the default one.
Is there a command to ignore the default embedded subtitles that can be used for Avisynth scripts?
MKVTools is my favorite for modifying tracks in MKVs on the Mac.
2x HDHomeRun Prime - 3CC
Sharp 65" TV; Sharp 46" TV; Panasonic 42" TV; Sony 40" TV; Sony 32" TV
WMC HTPC Server: Intel Celeron G1840, 4GB RAM, MSI H81M-P33, 1TB
Main HTPC: Mac Mini 2.3Ghz i5, 8GB RAM, 500GB, 1TB, 2TB, 3TB
XB360 WMC Extender, Ceton Echo, Roku 3, Apple TV 3
Just Google search "How to Remove Subtitles from MKV, AVI, MP4, etc without Hassle".
It can achieve different functions like delete subtitles from video, extract subtitles from MKV, AVI, VOB, MP4, AVCHD, FLV, MOV, MPEG, WMV, ASF, RMVB, DV, 3GP, etc.
I like it.