So, you have programmed the radio with the memory channel information you want and the repeaters require a 1750 tone for access. All worked well when you used the option in VFO, but now the function does not work properly in your memory channels... on the same frequency. What's up?
This Yaesu radio lets you set the Moni/TCall option for the menu key differently for each memory channel. See the screen shot from the main page of the FT991 programmer (it is the same for the 991A programmer). There is a column on the main sheet for Moni/TCall.

Be sure to set this option for the repeater in your memory channels.
This Yaesu radio lets you set the Moni/TCall option for the menu key differently for each memory channel. See the screen shot from the main page of the FT991 programmer (it is the same for the 991A programmer). There is a column on the main sheet for Moni/TCall.

- Unchecked will render the TCall function unavailable for that memory channel. When the menu button is pressed, the Moni (Monitor) function will be engaged allowing you to open squelch and listen to weak signals. .
- Checked, TCall is engaged which allows transmission of the 1750 tone needed for access to the repeater. You still must access the menu and the correct button of the menu, but now it will be active and the tone transmitted as expected (i.e., the button selection varies per operating mode.) The menu item can be set to a key via the options in the Settings file of the programmer.
Be sure to set this option for the repeater in your memory channels.