I always use Avidemux it's freeware, it can rotate and apply al lot of other filters and manipulations. Export to MP4 (MP4 muxer) using Mpeg4 AVC (x264) codec, use constant bitrate single pass 20000kbit/s this is similar quality as garmin virb output.
So I have figures out how to mount my virb at a 90 degree angle to give me the correct orientation. When i tack, the camera flips 180 degrees. When I hit the virb edit flip on my clip, it rotates my current clip AND the other clips that were part of the original file before I split. Is there an option I need to clip to only rotate my ACTIVE clip?