I used the branch ide-1.5.x that I pulled today.
I have made a few changes to Sketch.java, but it is unrelated to the issue.
My latest pull was a while ago on 1.5.3 version and the serial monitor was working fine.
I did notice there was a change from RXTX to jSSC that was reverted back, but there was no comments and I didn't quite understand why it was introduced and then reverted back.
Maybe it has something to do with this problem I'm getting.
You can see the history of the file here: