First, if your children are sick or have recently been sick with vomiting and diarrhea, I would AT LEAST DELAY their 2nd flu shot. I would never vaccinate a sick or teething child. When kids are sick or actively teething (like they're obviously in pain, chewing, drooling, bulging gums), their immune system is already working overtime. I would not personally add a vaccine to that mix - I'd wait until my kids were clearly healthy again before even considering flu shot #2.
Second, our family vaccinates on a very delayed plan and only selectively (we don't do multiple vaccines at a time in case our child would have a reaction so we'd know which shot was causing it). We also don't do all vaccines, only the ones we have researched and believe to be important - for example, one of the vaccines we do NOT get is the chicken pox vaccine (varicella/Varivax). We believe that it is more beneficial to actually catch chicken pox, recover (as the *vast* majority do), and have lifetime immunity - the chicken pox vaccine does not provide lifetime immunity.
At any rate, our family does not get the flu shot because:
* thimerisol (mercury preservative) is still used in the preparation of the flu vaccine and I do not want my young children to have even minute amounts of this, though some offices do have the thimerisol-free flu vaccine also available (if we got a flu vax, it would HAVE to be thimerisol free)
* we believe good hygiene (frequent hand washing, covering our mouths well if we cough or sneeze, etc.), eating healthfully (including probiotics), staying well hydrated, and getting adequate rest are more effective tools for fighting off the flu than getting a vaccine (http://www.mercola.com/2003/oct/29/flu_shot.htm)
* each year, the strains of flu that are in the vaccine are just a guess - yes, supposedly even if the flu that goes around is different than the ones given via vaccine, they say there's some protection despite the difference, but...? seems like there's a lot of uncertainty
Last, in general vaccinations are sort of considered "never at fault" by most medical professionals -- meaning that a decent number of reactions that are due to vaccines are often dismissed by doctors, nurses, etc., which is really awful if your child is having the reaction. I don't likw how the Vaccine Information Sheets (VIS) are "dumbed down" and tend to gloss over the comprehensive list of reactions, so I'd recommend asking for the actual vaccine insert that comes in the box of vaccines to see what are the more complete list of reactions, cautions, etc. You can see for yourself here how the 2 VIS for the different flu vaccines (one shot, one nasal spray) are so simple, but not necessarily very detailed or informative when it comes to a list of reactions reported by the people who have had the shot:
Vaccines are a tough decision, in my opinon, as there are clearly risks to getting them AND to not getting them. As a parent, my job is to weigh my family's risks of getting the disease (whether it be flu, chicken pox, pertussis, mumps, etc.) with the risks of the vaccine. I know many say that there are "no risks" to vaccines - but why do you think they make you sign your name giving permission to vaccinate your child each time? You're basically acknowledging that you agree that there are risks to vaccines, including severe injury or even death, and that you're releasing them of any responsibility. Yes, if you don't vaccinate, you MAY run the risk of you or your child catching the disease, but how likely is it that they'll get it? How bad would it be if they did get it (what are the statistical dangers, what percentage of cases are severe)? Is the danger of getting the disease less or more risky than the danger of a vaccine reaction?
See what I mean? In my mind, the question of "to vaccinate or not" is a very big grey area with no one perfect, right answer. Either way, there are risks. It's really just risk management. So, for your kids, you just need to check in with your mothering instinct and see what you think is best - delay the flu booster until they're healthy, or not get it at all, or get it as is currently scheduled. You'll make the right choice for your family, I'm sure, since you know them best!