Has the TOER register of MTU2a been set? Output from the MTIOCij pins of channels 3 and 4 (MTU3, MTU4) is disabled following the release of a reset. MTU output needs to be enabled using the TOER register.
Set MTU3 and MTU4 in the following order.
1. Set the CST3 and CST4 bits of the TSTR register to 0.
2. Set the TOER register.
3. Set the TIOR register.