I have noticed an errant behavior new in Mathematica 9. I thought at first it was because I was importing a very large text file and Mathematica just couldn't handle it. But now, I have seen the errata repeat with a relatively small ~13MB text file.
Once the file is imported, and you perform virtually any other command on the variable that is holding the imported data, Mathematica clears not only that variable but every other variable defined as if
had just been invoked!
Very frustrating! I have seen this repeat multiple times now and in version 8 this never happened.