Toilet bowl doesn't hold water but tank is full

Smells usually come from the tank and not the bowl.
Buy tank deodorizer from local store located near toilet brushes.
http://secure.willert.com/images/bf_wire.jpg
Deodorizer hangs inside tank. make sure it reaches the water.

You can also drain and clean the tank using CLR calcium lime and rust remover.
The CLR and gunk are fine for flushing away as long as the gunk doesn't clog the flush holes that let water flow into bowl.
http://www.fixya.com/support/r6633961-toilet_doesnt_flush_water_just_spins

Sewer line can also cause of odor.
If the toilet bowl is not full of water, or if nearby drain is not filled with water, or if toilet is not sealed tight against floor, or if toilet appears to have dampness visible around base, or if a vent pipe terminates behind a wall instead of on the roof: these things can cause sewer air to enter room.

Hi,
Reset the fill valve so that it does not fill the tank so full....this will be easier then trying to find a different flapper that will drop down faster, which is the only other thing you can do...

heatman101

The toilet you just installed is a 1.6 gallon flush water saver and will not have the same amount of water in it that your old 3.5 gallon toilet had. The water level may not be able to be raised as this is the nature of the beast.

If you can raise the level it will only be a little and will be done in the tank area by increasing the water level in the tank. If the water level in the tank is at the mark provided it a done deal.
The amount of water refilled into the bowl is done by the tube that runs from the fill valve into the overflow tube of the flush valve so if you put more water into the tank more water will be put into the bowl but the bowl will only hold as much water as the trap weir will let it hold (what the factory has sit it at and is not changeable

the tube that goes from the fill valve to the fill tube may not be installed correctly. the water must be going in the tube and not the tank. also it is a water conserving toilet so it uses less water also it is a comfort height toilet and to make it taller the bowl is extended so the water may seem even more shallow.

If I understand correctly, your water level inside the bowl is 3 or 4 inches from the top of toilet seat?
Sounds peculiar to have that water level since you would get splashing etc.
That is not sanitary, and would be a code violation.
Look at side profile of tank.
Look at porcelain behind bowl and you can see outline of "s trap."
This is the internal trap that each toilet has built in.
Purpose of trap is to a) set water level inside bowl and b) just like a sink trap, seal pipe from sewer air from entering home.
Photo shows trap on sample toilet, with line showing approximate level of water inside bowl.
Since photo is at an angle, the line appears to go downward instead of level. Again the line is approximation, and photo intended to show where you can look on your toilet.
Your tank should have similar s-trap feature. From the feature on your tank, you can see what level water is intended to be inside bowl.
Some more expensive tanks, outline of s-trap is not apparent.

If the water level is so high that you experience unsanitary conditions, this is a code violation, and toilet should be replaced.

Quick web search turned up Kohler contact page: http://www.us.kohler.com/general/contact.jsp
KOHLER Customer Care at
Phone: 1-800-4KOHLER (1-800-456-4537)
Hours: 8:00 AM - 5:00 PM (Central Time) Monday to Friday
You can refer Kohler to this link on Fixya so they can clearly understand issue.

The small black tube that goes into the overflow is used to fill the bowl after flushing. Would check to make sure that water is coming out of that tube at full force or if its coming out at all.

Alot of times this problem occurs when there is not enough water in the tank behind the seat and bowl. Lift off the tank lid and see how much water is it, It should be near full.If it is not your problem is not enough water.

is the black thing between the the tank and the bowl?
if so, go to any of the home center or plumping store for the seal.
shunt off the water and unbolt the 3 bolts that holds the tank to the bowl from the buttom. you may need a flat screw driver to help hold the bolts. pull up the tank slowly, and lay it on the side, replace the seal, reseat the tank on to the bowl and tighten the bolts. make sure all bolts are equal pressure and the tank is level.