I would first try to identify 1 single unaligned photo that you think has sufficient overlap with at least 2 of your 390 aligned photos, and post it here along with the 2 aligned ones so see if anyone can identify why it didn't work.
One possible reason is insufficient overlap, but you did say it was high so it might not be that.
Another possibility is that 'generic preselection' didn't identify those particular images as a good match (because it only looks at lower resolution versions to work out the pairs) and so it never tried to align them. You could test that by using a smaller number of images (a handful from the 390 aligned, and a handful of close but unaligned neighbours from the rest) in a chunk with all preselection disabled (because that's much slower) just to check if the images do overlap enough.
If that works, then you could try grouping your photos into chunks of ~400 that do align with generic preselection, and then some connecting chunks of fewer, but definitely overlapping, images which can be aligned with preselection disabled, and then once you have everything aligned in separate chunks you can align the chunks by 'cameras' and then removing the connecting chunks and merge the rest, and optionally do tools -> tie points -> build tie points to generate actual matches between the groups, but this is getting a bit advanced and if you've had to go to these lengths to get here then it's likely that your images aren't very good or the overlap is inadequate and so results may still be poor.