The majority of timeout errors with serial, occurs during a read. You specify x number of bytes to be read. The read will terminate when that number of bytes have been read, when the termination character is detected, or when the timeout is reached. The detection of a term character is the default setting and the default term character is a LF. If term character detection is off, the read will wait until the number of bytes have been read or the timeout is reached. The timer starts when the Read is first started. So, you could get a timeout if there is nothing in the serial recieve buffer (instrument has sent nothing), there are fewer bytes in the buffer but no termination character (or different than what is expected), or simply fewer bytes in the buffer.
Serial timeout errors can also occur when you use handshaking. These can happen on a read when the instrument on the other end does not assert the handshake lines.
