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GPS.4 / P9.21 and SPI1.4 / P9.29 are two mux options for the same signal (ehrpwm0b), hence if you mux both of them to pwm, they will both output the same signal.

Same goes for GPS.3 / P9.22 and SPI1.5 / P9.31, which are two mux options for ehrpwm0a.

Here's an overview of all PWM resources on the AM335x and to which connector pin or on-board resource of the beaglebone blue they can be muxed:

eCAP 0: S1.2.6 (net SPI1_SS2, pin 89, ball C18, gpio 0.07, BBB P9.42a)

eCAP 1: UT0.4 (net UART0_TX, pin 93, ball E16, gpio 1.11, BBB serial console rxd)

eCAP 2: two options:
UT0.3 (net UART0_RX, pin 92, ball E15, gpio 1.10, BBB serial console txd)
GP0.6 (net GPIO3_17, pin 103, ball C12, gpio 3.17, BBB P9.28)

pruss eCAP: two options:
E4.4 (net PRU_E_B, pin 15, ball U13, gpio 1.15, BBB P8.15)
S1.2.6 (net SPI1_SS2, pin 89, ball C18, gpio 0.07, BBB P9.42a)

eHRPWM 0a: two options:
GPS.3 (net UART2_RX, pin 84, ball A17, gpio 0.02, BBB P9.22)
S1.1.5, S1.2.5 (net SPI1_SCK, pin 100, ball A13, gpio 3.14, BBB P9.31)

eHRPWM 0b: two options:
GPS.4 (net UART2_TX, pin 85, ball B17, gpio 0.03, BBB P9.21)
S1.1.4, S1.2.4 (net SPI1_MISO, pin 101, ball B13, gpio 3.15, BBB P9.29)
eHRPWM 1a: M1 pwm (net PWM_1A, pin 18, ball U14, gpio 1.18, BBB P9.14)
eHRPWM 1b: M2 pwm (net PWM_1B, pin 19, ball T14, gpio 1.19, BBB P9.16)
eHRPWM 2a: M3 pwm (net PWM_2A, pin 8, ball U10, gpio 0.22, BBB P8.19)
eHRPWM 2b: M4 pwm (net PWM_2B, pin 9, ball T10, gpio 0.23, BBB P8.13)

timer 4: two options:
GP1.5, USR RED led (net LED_RED, pin 36, ball R07, gpio 2.02, BBB P8.07)
WIFI led (net WIFI_LED, pin 108, ball A15, gpio 0.19, BBB hdmi 24M clock)
timer 5: none
timer 6: none
timer 7: GP1.6, USR GRN led (net LED_GRN, pin 37, ball T07, gpio 2.03, BBB P8.08)