A method for handling input/output (I/O) commands in a storage system includes establishing first and second counters for counting unfinished I/O commands, and establishing a reference which is initially set to the first counter. The reference is periodically switched between the first counter and the second counter, and the switching interval is less than the I/O timeout value. Upon placing an I/O command into an I/O command queue, a copy of the current reference is made into an I/O specific control block and the current referenced counter is incremented. Upon finishing of an I/O command, the counter referenced by the I/O specific control block is decremented and the I/O command is removed from the I/O command queue. When switching the reference, a problem is detected in the event that the counter being switched to is above a predetermined threshold. Upon detection of a problem, a more explicit I/O check is conducted.