The MicroAPRS firmware for MicroModem supports changing AX.25 settings like preamble length, TX tail and others via the KISS protocol, so the host program can easily set these parameters. Unfortunately some programs, Xastir in particular, will send a reset to the modem when opening the serial port, and then immediately send the configuration commands. If your modem is using a bootloader (which allows it to be programmed via avrdude and the Arduino IDE over USB), these configuration commands will end up being read by the bootloader as the modem is starting up, instead of being read by the MicroAPRS firmware, and thus resulting in the parameters never getting set.
Luckily, there is a simple fix for this, if your host program does not allow disabling the resetting. You can simply connect a small resistor between the "VCC" and "DTR" pins on the modem, a value around 100 ohms should do. In this picture I used an 80 ohm resistor.
When the resistor is connected, the reset line cannot be activated, and the modem will thus not be rebooted by the host. It's important to note that you will need to take out the resistor if you want to flash another firmware onto the modem, since the flashing process requires a reset signal to be sent to the processor.
Using KISS settings in Xastir