If indexing it with the ffmsindex.exe isn't working, then the next best thing you could try is splitting the mkv/mp4/whatevs it is first, and loading it separately.
Drag and drop the video in mkvmergegui, go to the global tab and check "enable splitting", then you can do after this size and you can pick the preset that most suits your taste or specify your own. Considering you have issues with 8GB+ files, I guess you could use the 4483M preset, which is 4 GB or so. Then click start muxing and you'll get a bunch of mkv. Index them separately first (if ffmsindex.exe doesn't work as intended as it seems to have been evidenced above, just make an avs for each) and after that is done, make a single avs like so:
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ffvideosource("blabla-001.mkv")+ffvideosource("blabla-002.mkv")+ffvideosource("blabla-003.mkv")
which will give you the whole thing in a single avs.
Not the prettiest solution, but it should work as intended. Better than nothing.