I was having the same problem. Here is how I solved it:
Set the proper working directory where your tree is located:
Read the tree into R using Ape:
tree <- read.tree("dayhoff_bpcomp.con.tre")
Write the tree to an output file using Ape:
write.tree(tree, file = "tree.newick.tre")
I'm not sure why this works, as I cannot see any meaningful difference between the original tree and tree.newick.tre, they even have the same number of characters! However, once I went through these steps, figtree had no problem opening the tree.