Unwanted strobe effect showing on rendered clips - Adobe CC 2014

I'll try and describe the issue as best as possible - I haven't been able to find any similar issues by googling or on forums.
As a bit of information about the project it's adobe CC 2014 with a mix of c100, c300, Gopro and various other footage so a mix of .MTS, .MXS and Mp4 files. All stored and edited from external hardrive via USB 3.
I started out by having red frames appear when I scrubbed through footage on the timeline, and then they appeared in the actual exported file - which from googling seemed to an issue with media encoder not being able to render the source clip properly.
As part of the fix which seemed to work to get rid of the red frames I moved the media cache files from their default location users>library>applicationsupoprt>adobe>common to a render folder which I created on the external hardrive. To be specific I manually deleted media cache and media cache files then created the folder on the external drive and directed adobe to put the files there. That got rid of the red frames but a few days and a different project later I started getting a strobe like effect where every other frame on a few (seemingly random) clips is black, except for the top left corner which shows the image in part. When the footage is unrendered (red on timeline) it plays back fine. When it's rendered the strobe effect happens everytime on playback and with export. All clips it happens to are c300 clips, but there are plenty of c300 clips in the timeline it doesn't happen to. All clips have the same effects on them.
I've made all clips offline, and reconnected media. I've uninstalled and reinstalled adobe CC desktop and all apps about 3 times and used Adobe cleaner to get rid of files then reinstalled. Nothing seems to work. I have noticed that even though the media cache files are redirected to the external drive now, it still creates a media cache folder in the default location and puts some render files there. Perhaps it's something to do with these duplicate render files???
Hope that makes some sense.
Anyone else had this happen?
Any help/advice would be much appreciated. It's for a TVC and needs to be delivered next week.

Thanks Simon, I think you're right.
I seem to have narowed ig down to being a combination of the 'warp stabilisation' effect plus a vignette (made from black video and 'circle' effect).
Whenever these effects are both on, and the clips are rendered I get the strobe effect, but if one or the other is off I don't anymore.
At least I can export the edit with warp stabilisation effect, and then add the vignette to the exported clip - not ideal but a work around.
Hope it get's fixed soon.

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