My two year old is running a fever of 102.3 I am giving Tylenol and motrin ever 3-4 hours and when the med wears off the fever comes back... dr said everything was fine on him today... what is causing this? He has a runny nose and watery draining eyes.

It could be a number of things, if the doctor is not concerned you have two choices. Continue doing what you're doing until his fever breaks or get a second opinion. You're still concerned even though your doctor isn't so maybe find a second opinion? A walk in clinic?

The meds for the fever won't make the fever go away permanently, they are to help lower it for your child to be comfortable. Once it does wear off, if your child is still fighting an infection the fever will be back. It actually is natures way of helping to fight the infection. He may have it for a few days, which wouldn't necessarily be uncommon.

How is he doing otherwise? Is he still eating fairly well? Does he still play? He may be more tired, but is he generally his usual self? Those types of things can be a better indicator of how he is feeling than his temp.

As CravenMorhead said, you can always take him to another doctor, or see how he does and contact your own doctor again if you feel he hasn't improved, or certainly if he seems to feel worse, in the next few days.

Toddlers run higher fevers than adults.
Reduction of fever by Tylenol and Motrin is a good sign. Yes, it's temporary - just as it is in adults. The first thing you would expect is an ordinary virus cold. Anything after that is 'wait and see,' keeping a close watch.
I would get a book or two out of the library about typical childhood conditions and symptoms, or spend a few days searching key terms such as 'toddler fever' and 'child cold symptoms.'
If you don't feel that your doctor chats enough about all this, tell him so.