I now recall this problem during my last update also.  After clicking update (force and logging were unchecked) I begin getting error 116 from line 599 of wtasinit.src .It is an error creating file.  I have to click an ok button on each occurrence to continue. It appears to be all filenames of the pattern IS*.B99.  Anyone have ideas?
 
A bit of additional info - there were a couple of BK files also. But now I'm stuck on the Update 05/27/09 screen after a write violation error with the filename of ISNUMBER.B99 on the screen.

update problem continues while trying to come up to the 18 Jan 2011 update.
 
When I tried to create the 99 company in the testdata directory I realized that I did in fact have a testdata directory with b99 files in it already.  Just comparing it to our live company it has about 100 files fewer.  So an add company won't work because 99 is already in the dictionary.  I tried to delete it so I could add a fresh 99 company but get an error opening BKSYMSTR.B99 - 94 followed by the access of file not previously opened FNUM =0.
 
So my current only option for doing an update it to wait for the error on each b99 file then at the end know that isnumber.b99 is the last one and use task manager to kill the process which is hung at that point (very bad and unsettling method me thinks)
 
Can someone give me some details on manually straightening this out?

I figured this was a Lynn question.  Thanks for picking up on it.  I'll let you know if I have any problems.