I found that certain path/filenames were not valid with the latest jfs release.
I had a problem with eCSMT where the file ecsmt_desc.lst was not being unzipped from the ecscntl.zip file. Then I found that I could not launch Lotus Notes because e:\lotusw4\notes\data was not being found correctly somehow. Neither of these alone made me think of the jfs update but then I went to do a cvs pull for Mozilla and almost immediately got an error that e:\cvs\work\mozilla\.cvsignore was not valid. The three issues then dawned on me that they were related and I backed out to the 3/17 release and the problems went away.
There was no error on the first issue, ecsmt_desc.lst just didn't appear when I unzipped the file but it was in the zip file (I was able to copy ecsmt_de.lst to ecsmt_desc.lst without error).
The second case just gave me a Lotus Notes Error that the data directory could not be found.
The third one was an invalid filename if I remember correctly but unfortunately I wasn't able to get logged on here due to my id issues. I can reproduce it later this week for an exact error message.