I just found a bug with this mod that I guess has to do with recent changes with Factorio 1.0+. In particular, the modded rails(I've only tested with the stone brick rails, but I assume this is the case with all three) don't properly interact with cliffs. I currently have a locomotive parked in the middle of a cliff on top of the modded rail, where I was unable to place/ride a normal rail.

I assume this has something to do with the collision mask.

Do you play with "Transport Drones" by any chance? I've got the same behavior, and reported it more than half a year ago per PM (as yet unread) in the forum.

Basically, Transport Drones removes "object-layer" from the collision mask (Klonan: "I change the collision layer of the rails so that you can build rails on the transport drone roads. Adding object layer to the rails will mean that they cannot be built on the roads, which severely impacts the usage."). But the bridges have only "object-layer" in their mask to begin with, so if Transport Drones is active, they have an empty collision mask and can be placed anywhere.

@kapaer:
I've had the same problem with the wooden rail bridges in Bio Industries. Solution: Add another layer from the rail's default layers to the collision mask of the bridges. I've used "floor-layer" in the 0.18/1.0 branch and "rail-layer" for 1.1.

Since versions 0.18.33/1.1.3, I set the collision mask of all known bridges (so far, just BI's and yours) as explained above in data-final-fixes. I also set fast_replaceable_group to data.raw["straight-rail"]["straight-rail"].fast_replaceable_group or "rail", so BI's wooden rail bridges can be easily updated to one of your bridges. If you think this could break something on your end, just say so, and I'll try to make changes according to your needs. :-)