On HDToolBox there is a button called "verify data on drive".
What it does? Check the entire drive for bad clusters (or a problem in the surface of the drive.
It's a veeeeery long operation (some like 6~22 hours to perform in a 4Gb drive), but after that the parts of the drive with problems will not used anymore (saving you from real problems).
Also Quarterback Tools use a different approach: the "sub-program" checks the files, when it found a bad "cluster", it move the file from there and assign the bad cluster to a dummy file (read-only and hidden).
BTW: using another file systems you don't have the problems you mention.
