I do have show the show hidden files option on, but the 2 files aren't hidden files anyway, but they don't show up in 4.2.1 build 428. They do show in 3.8.2 build 330 and the latest version of psftp though. They are the 2 latest files in the directory. I tried quiting and opening the connection again, but the files still don't show.
I've made a log file. Would it be possible to send the log file to directly to you, without posting it, if you want it?
BTW the log doesn't show the files that are missing from the display. At least not in the "Read file X from listing" section.