I think from the waveforms you showed it appears that you are having problems with bootstrap capacitors 20uF shown in your driver schematics http://www.8052.com/users/monish/driver%20ckt.JPG
Bootstrap capacitors values need to be calculated accurately taking into consideration the switching frequency of the PWM.
These bootstrap capacitors provide the VCC of the gate drive for the upper IGBTs. They charge up when the corresponding lower IGBT is switched on so you have to make sure that lower IGBT is switched on long enough for them to charge up to +15 VDC and not 12VDC as mentioned below. They also need to be able to sustain their voltage during the upper IGBT on period and not discharge.
I think you should consider these points:

1. You need to use +15VDC to the gate drive circuitry and not 12VDC to make sure upper IGBTs switch fully on and bootstrap capacitors sustain a voltage more than 12VDC during the upper IGBT on period because they start discharging.
2. At start up you need to switch the 3 lower IGBTs on at the same time while the 3 top IGBTs are off to start charging the bootstrap capacitors to supply Vcc to upper IGBT gate drive circuits. You work out the time it requires for these capacitors to charge up. The datasheet for IR2112 recommends 10uF capacitors but you used 20uF and you use higher PWM frequency which might not be enough to keep these capacitors charged. I recommend you try 10uF or even lower depending on your calculation and or simulation.
3. Look carefully at the optocouplers you use, they tend to distort the signal because they have different switch on and switch off times (check datasheet for details). This will be a major problem at high switching PWM frequencies and I recommend you remove them from your circuit because they are not needed in this configuration.
Do these things and come back with results. IGBTs are very interesting.