Juan,
There could be a couple different things going on here.
1. When you added the decimation into ADC1_IRQHandler the KMS tool didn't take that into account when it calculated the gains.

KMS provides a way to do that decimation so that it will account for it correctly in the gain calculations. The PWM / Fast ISR is used for this purpose. We've ran up to 80kHz PWM with a divider of 4 successfully on the TWR eval kit.
2. If you are not using the reference hardware make sure that your power device is configured correctly. When you get into high speeds you are also at high modulations and if the deadtime isn't configured correctly this will destroy your power devices. See AN5254 for more information.