Hope This Helps
Hmmm Val, It could be something under the roadbed and thats a shame 'cause it alreadys seniced. If you think thats where it is then the only thing to do is pull it up and see. The only other thing that I can see is maybe there is something under the ties right there at that joint. If you have got a thin blade putty knife try running it under the ties and see if anything is there.
My next thought is that the roadbed (homasote) is not the same thickness as the ajoining peice. Homasote is a "nominal" thickness and can vary from batch to batch as it is manufactured. If this is the case then just some sanding will bring it back into the proper thickness.
My next thing is the railjoiners could be deformed. Place some flat like a file across the joint and push down firmly and see if the joint doesn't even up. If it does drill a small hole in the center of the end tie of each piece of track. Then while holding down on the joint put a track nail or a spike into the hole and push it down to hold the joint in place.
As for cleaning up, the shop vac will do the job but you'll have to do some touch up on the ballast and the ground cover.
This is one of those problems that rears its ugly head from time to time
I don't reccomend filing down the rails to cure the problem. That just makes a dip in the rails. I'd rather do it the hard way and find the cause of the problem