Our autosampler has a volume of 15 microliters between the tip of the needle and the injection valve. This can result in the sample loss, dilution or carry over depending on the injection mode. (However, this layout of valve and needle is a huge advantage to making the system more robust. Similar, or even more complicated, problems can happen with other needle and valve designs.)
The advantage of partial loop injections is that they are quick, the most accuracy, and can rinse (flush volume) the needle tubing with the sample before the injection. The major disadvantage is wasting sample. (equal to the set flush volume). Extra sample volume is aspirated from the sample during each inject and never loaded on the column. The flush volume washes the needle before the injection and the needle remains in the sample vial until the injection is made which means that sample is left in the needle and will be discarded during the wash cycle. Even if the flush volume is set to zero, the first 15ul of whatever the injection volume is set to will actually be injected in place of the sample. This will be waste solution. 15ul should be the minimum flush volume, but be aware that the smaller this volume, the greater the amount of wash fluid that may be contained in the injection because of tailing. The inclusion of an air gap ahead of the flush volume, can reduce the problem of tailing.
The microliter method's major advantage is zero sample loss. As you can see in the manual, the sample segment is sandwiched between two mobile phase segments and drawn into the center of the injection loop. This process means that the sample tailing is compensated for. The segment of mobile phase behind the sample segment serves to thoroughlyl wash the needle. The disadvantage is that the maximum injection volumne with the standard 100ul sample loop installed is only 27 ul per injection. It should also be noted that when using this method, the same batch of mobile phase must be use as wash fluid because it will be injected. The solution will most likely contain salt which has to be thoroughly wash out of the autosampler at the end of your analysis to avoid damaging the autosampler. (This method does not accept flush volume even if you enter it because the first mobile phase segment picked up serves this function.)