That’s sounds like you have the receive audio connected to discriminator audio out of the Alinco. Is there another pin that has squelched audio? If so try that as it would be your best option. If there is no other pin you can use for audio output, try using simple-tune-menu to set de-emphasis to on. That may correct the audio characteristics to help the DTMF issue. Also it will probably make your audio sound less tinny to connected nodes.
Another thing that will often help DTMF decoding is to turn on the CTCSS Rx filter.