Thanks, I've used the same settings in u-boot and Linux.
/debug/omap_mux # cat i2c0_scl
name: i2c0_scl.i2c0_scl (0x44e1098c/0x98c = 0x0070), b NA, t NA
mode: OMAP_MUX_MODE0 | AM33XX_PIN_INPUT_PULLUP | AM33XX_SLEWCTRL_SLOW
signals: i2c0_scl | NA | NA | NA | NA | NA | NA | gpio3_6
/debug/omap_mux # cat i2c0_sda
name: i2c0_sda.i2c0_sda (0x44e10988/0x988 = 0x0070), b NA, t NA
mode: OMAP_MUX_MODE0 | AM33XX_PIN_INPUT_PULLUP | AM33XX_SLEWCTRL_SLOW
signals: i2c0_sda | NA | NA | NA | NA | NA | NA | gpio3_5
/debug/omap_mux #