I guess that your timer is initialized by settings in the properties.
Leonardo and Micro uses a 32U4 chip and cdc_acm communication protocol. I think you must set Rts=1 to enable transmit from the 32U4. This signal is not available in the built in serial component, so I recommend that you use my extension instead as discussed here: Using serial with FTDI
You can find the extension and some documentation here:
The functions of this extension will hopefully be included in AppInventor in the future.
I hope this will solve your problems.
Good luck
Rkl099