On my machine, a command like "C:\Documents and Settings\Tim\My Documents\test1>perl readdir.plx" doesn't work (produces a "Bad Command" error.)
Try "perl readdir.plx < C:\Documents and Settings\Tim\My Documents\test1" (or maybe a pipe instead of the ">").
That may be unrelated to your problem, though. As I mentioned in a previous reply, I think your last foreach loop is logically garbled. Why are you operating on the files in dismissed2.txt for each $f in @thefiles? And won't that just work for the first $f? (You will have reached end of file in dismissed2.txt after that.) (That may also be unrelated to the specific error you mention, though...)
chas