Peculiar. Tested here just now, subtitles looked fine in MPC-BE, which is similar to VLC. When the sub window is opened are they all there? What VP version?
Upload one of the projects that has the problem and we'll check it out. This is easy, quick and can be private. Don't upload the export - just the PORTABLE PROJECT folder, and link it here.
Follow these instructions...
http://nch.invisionzone.com/topic/23659-tips-for-getting-help-on-this-forum/
If it contains sensitive material link it in a personal message (PM). Click the envelope above. It won't be passed on or retained. Use FILE|SAVE PORTABLE PROJECT AS, not simply SAVE PROJECT, and don't forget to get a shareable, public link - not one that is restricted.