If you have a secondary redstone source to power lockdown tracks they will sometimes not accept being powered by the unloaders. In the example in the picture I have a goods train and I use an any detect to invert (turn off) the lockdown tracks once the locomotive has finished pulling up to the unloading station. Occassionally some of the unloaders on two of such stations will not light up after the operation has been completed (some are set to immediate, some are set to Complete).

I've also tried this with vanilla repeaters powering the tracks, same issue.

Need more details. Give me some annotated pictures of the simplest setup you can create that duplicates the problem (using only railcraft and vanilla).

Here's a video explanation using only vanilla redstone: http://youtu.be/yWgG7_ByEiA

Is a block update adjacent to the track sufficient to "fix" the issue? IE. place a block down next to it.

I suspect some kind of update race issue where the two sources are interfering.

Also since it doesn't appear to be an easy fix, I'd recommend setting the loaders to manual and using some kind of timer to control when the train stops and when it leaves.